Andrej Sali, PhD

Title(s)Professor, Bioengineering
SchoolSchool of Pharmacy
Address1700 4th Street, #503B
San Francisco CA 94158
Phone415-514-4227
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    Collapse Biography 
    Collapse Awards and Honors
    Science Ambassador of Republic of Slovenia2007Zois Award
    2000  - 2003Irma T. Hirschl Career Award Scientist
    1998  - 2000Alfred P. Sloan Research Fellow
    1996  - 1999Alexandrine and Alexander L. Sinsheimer Scholar
    1991  - 1994Jane Coffin Childs Memorial Fund for Medical Research Postdoctoral Fellow
    1989  - 1990Merck Sharp & Dohm Academic Scholarship
    Research Council of Slovenia1987  - 1988Scholarship for Graduate Studies
    Committee of Principals and Vice Chancellors, England1987  - 1990Overseas Research Students Award
    Birkbeck College, London, UK1987British Council Visiting Student
    Birkbeck College, London, UK1985British Council Visiting Student
    J. Stefan Institute, Ljubljana, Slovenia1984  - 1987Undergraduate Scholarship
    2018Fellow, National Academy of Sciences

    Collapse Overview 
    Collapse Overview
    Dr. Andrej Sali is interested in using computation grounded in the laws of physics and the theory of evolution to study the structure and function of proteins. His lab aims to improve and apply methods for predicting the structures of proteins, determining the structures of macromolecular assemblies, and annotating the functions of proteins using their structures. This research contributes to structure-based functional annotation of proteins and thus enhances the impact of genome sequencing, structural genomics, and functional genomics on biology and medicine.
    Collapse Websites

    Collapse Research 
    Collapse Research Activities and Funding
    High Performance Computer for Computational Biosciences
    NIH S10OD021596Jul 1, 2016 - Jun 30, 2017
    Role: Principal Investigator
    Mapping the conformational cycle of transmembrane transporters
    NIH P01GM111126Aug 1, 2015 - Jul 31, 2020
    Role: Co-Investigator
    The Yeast Centrosome - Structure Assembly & Function
    NIH P01GM105537Sep 1, 2014 - Aug 31, 2020
    Role: Co-Investigator
    Center for Structure of Membrane Proteins
    NIH U54GM094625Sep 30, 2010 - Jun 30, 2016
    Role: Co-Investigator
    High Performance Computing Cluster for Bioimaging and Computational Biology
    NIH S10RR027100Mar 18, 2010 - Mar 17, 2011
    Role: Principal Investigator
    IMP: Software for Hybrid Determination of Macromolecular Assembly Structures
    NIH R01GM083960Apr 1, 2008 - Aug 31, 2025
    Role: Principal Investigator
    NYSGXRC:A Large Scale Center for the PSI
    NIH U54GM074945Jul 1, 2005 - Jun 30, 2011
    Role: Co-Investigator
    Pharmacogenomics of Membrane Transporters
    NIH U19GM061390Apr 1, 2000 - Jun 30, 2015
    Role: Co-Investigator
    Comprehensive Biology: Exploiting the Yeast Genome
    NIH P41RR011823Sep 30, 1996 - Jun 30, 2016
    Role: Co-Investigator
    Protein Modeling by Satisfaction of Spatial Restraints
    NIH R01GM054762Jun 1, 1996 - Jun 30, 2010
    Role: Principal Investigator
    PROTEIN MODELING BY SATISFACTION OF SPATIAL RESTRAINTS
    NIH R29GM054762Jun 1, 1996 - May 31, 2001
    Role: Principal Investigator
    Targeting Cysteine Proteases: Antiparasitic Chemotherapy
    NIH P01AI035707May 1, 1995 - May 31, 2010
    Role: Co-Investigator
    3 D Electron Microscopy of Macromolecules
    NIH P41RR002250Mar 1, 1985 - Dec 31, 2014
    Role: Co-Investigator
    Degenerative and Dementing Diseases of Aging
    NIH P01AG002132Jan 1, 1981 - Mar 31, 2025
    Role: Co-Investigator
    A Synchroton Radiation Structural Biology Resource
    NIH P41RR001209Mar 1, 1980 - Feb 28, 2015
    Role: Co-Investigator
    Natl Resource for Mass Spectrom of Biolog Macromolecules
    NIH P41RR000862Dec 1, 1976 - Mar 31, 2012
    Role: Co-Investigator
    Resource for Biocomputing, Visualization, and Informatics
    NIH/NCRR P41RR001081Jun 1, 1976 - Sep 14, 2012
    Role: Co-Investigator

    Collapse ORNG Applications 
    Collapse Academic Senate

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Making fluorescence-based integrative structures and associated kinetic information accessible. Nat Methods. 2024 Sep 30. Hanke CA, Westbrook JD, Webb BM, Peulen TO, Lawson CL, Sali A, Berman HM, Seidel CAM, Vallat B. PMID: 39349602.
      View in: PubMed   Mentions:    Fields:    
    2. Structure and inhibition mechanisms of Mycobacterium tuberculosis essential transporter efflux protein A. bioRxiv. 2024 Sep 05. Khandelwal NK, Gupta M, Gomez JE, Barkho S, Guan Z, Eng AY, Kawate T, Balasubramani SG, Sali A, Hung DT, Stroud RM. PMID: 39282303; PMCID: PMC11398473.
      View in: PubMed   Mentions:
    3. The molecular architecture of the nuclear basket. Cell. 2024 Sep 19; 187(19):5267-5281.e13. Singh D, Soni N, Hutchings J, Echeverria I, Shaikh F, Duquette M, Suslov S, Li Z, van Eeuwen T, Molloy K, Shi Y, Wang J, Guo Q, Chait BT, Fernandez-Martinez J, Rout MP, Sali A, Villa E. PMID: 39127037; PMCID: PMC11416316.
      View in: PubMed   Mentions: 3     Fields:    Translation:AnimalsCells
    4. Integrative spatiotemporal modeling of biomolecular processes: application to the assembly of the Nuclear Pore Complex. bioRxiv. 2024 Aug 08. Latham AP, Tempkin JOB, Otsuka S, Zhang W, Ellenberg J, Sali A. PMID: 39149317; PMCID: PMC11326192.
      View in: PubMed   Mentions:
    5. Multiscale photocatalytic proximity labeling reveals cell surface neighbors on and between cells. Science. 2024 Jul 19; 385(6706):eadl5763. Lin Z, Schaefer K, Lui I, Yao Z, Fossati A, Swaney DL, Palar A, Sali A, Wells JA. PMID: 39024454.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    6. Cell Maps for Artificial Intelligence: AI-Ready Maps of Human Cell Architecture from Disease-Relevant Cell Lines. bioRxiv. 2024 May 24. Clark T, Mohan J, Schaffer L, Obernier K, Al Manir S, Churas CP, Dailamy A, Doctor Y, Forget A, Hansen JN, Hu M, Lenkiewicz J, Levinson MA, Marquez C, Nourreddine S, Niestroy J, Pratt D, Qian G, Thaker S, Bélisle-Pipon JC, Brandt C, Chen J, Ding Y, Fodeh S, Krogan N, Lundberg E, Mali P, Payne-Foster P, Ratcliffe S, Ravitsky V, Sali A, Schulz W, Ideker T. PMID: 38826258; PMCID: PMC11142054.
      View in: PubMed   Mentions:
    7. Illuminating the function of the orphan transporter, SLC22A10, in humans and other primates. Nat Commun. 2024 May 23; 15(1):4380. Yee SW, Ferrández-Peral L, Alentorn-Moron P, Fontsere C, Ceylan M, Koleske ML, Handin N, Artegoitia VM, Lara G, Chien HC, Zhou X, Dainat J, Zalevsky A, Sali A, Brand CM, Wolfreys FD, Yang J, Gestwicki JE, Capra JA, Artursson P, Newman JW, Marquès-Bonet T, Giacomini KM. PMID: 38782905; PMCID: PMC11116522.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    8. Nanobody repertoire generated against the spike protein of ancestral SARS-CoV-2 remains efficacious against the rapidly evolving virus. Elife. 2024 May 07; 12. Ketaren NE, Mast FD, Fridy PC, Olivier JP, Sanyal T, Sali A, Chait BT, Rout MP, Aitchison JD. PMID: 38712823; PMCID: PMC11076045.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
    9. Identification of thrombosis-related conformational binding epitopes on domain I of β2-glycoprotein I. Thromb Res. 2024 May; 237:145-147. Kim SJ, Schneidman-Duhovny D, de Groot PG, Urbanus RT, Carter L, de Laat-Kremers R, Weiss TM, Chan MK, Sali A, Rand JH, de Laat B. PMID: 38593525.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    10. The Molecular Architecture of the Nuclear Basket. bioRxiv. 2024 Mar 28. Singh D, Soni N, Hutchings J, Echeverria I, Shaikh F, Duquette M, Suslov S, Li Z, van Eeuwen T, Molloy K, Shi Y, Wang J, Guo Q, Chait BT, Fernandez-Martinez J, Rout MP, Sali A, Villa E. PMID: 38586009; PMCID: PMC10996695.
      View in: PubMed   Mentions:
    11. IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods. J Mol Biol. 2024 Sep 01; 436(17):168546. Vallat B, Webb BM, Westbrook JD, Goddard TD, Hanke CA, Graziadei A, Peisach E, Zalevsky A, Sagendorf J, Tangmunarunkit H, Voinea S, Sekharan M, Yu J, Bonvin AAMJJ, DiMaio F, Hummer G, Meiler J, Tajkhorshid E, Ferrin TE, Lawson CL, Leitner A, Rappsilber J, Seidel CAM, Jeffries CM, Burley SK, Hoch JC, Kurisu G, Morris K, Patwardhan A, Velankar S, Schwede T, Trewhella J, Kesselman C, Berman HM, Sali A. PMID: 38508301; PMCID: PMC11377171.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    12. In situ structure of actin remodeling during glucose-stimulated insulin secretion using cryo-electron tomography. Nat Commun. 2024 Feb 12; 15(1):1311. Li W, Li A, Yu B, Zhang X, Liu X, White KL, Stevens RC, Baumeister W, Sali A, Jasnin M, Sun L. PMID: 38346988; PMCID: PMC10861521.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    13. Nanobody repertoire generated against the spike protein of ancestral SARS-CoV-2 remains efficacious against the rapidly evolving virus. bioRxiv. 2024 Jan 29. Ketaren NE, Mast FD, Fridy PC, Olivier JP, Sanyal T, Sali A, Chait BT, Rout MP, Aitchison JD. PMID: 37503298; PMCID: PMC10369967.
      View in: PubMed   Mentions:
    14. Structural basis of prostaglandin efflux by MRP4. Nat Struct Mol Biol. 2024 Apr; 31(4):621-632. Pourmal S, Green E, Bajaj R, Chemmama IE, Knudsen GM, Gupta M, Sali A, Cheng Y, Craik CS, Kroetz DL, Stroud RM. PMID: 38216659; PMCID: PMC11145372.
      View in: PubMed   Mentions: 1     Fields:    
    15. Integrative spatiotemporal map of nucleocytoplasmic transport. bioRxiv. 2024 Jan 02. Raveh B, Eliasian R, Rashkovits S, Russel D, Hayama R, Sparks SE, Singh D, Lim R, Villa E, Rout MP, Cowburn D, Sali A. PMID: 38260487; PMCID: PMC10802240.
      View in: PubMed   Mentions:
    16. Structures, functions and adaptations of the human LINE-1 ORF2 protein. Nature. 2024 Feb; 626(7997):194-206. Baldwin ET, van Eeuwen T, Hoyos D, Zalevsky A, Tchesnokov EP, Sánchez R, Miller BD, Di Stefano LH, Ruiz FX, Hancock M, Isik E, Mendez-Dorantes C, Walpole T, Nichols C, Wan P, Riento K, Halls-Kass R, Augustin M, Lammens A, Jestel A, Upla P, Xibinaku K, Congreve S, Hennink M, Rogala KB, Schneider AM, Fairman JE, Christensen SM, Desrosiers B, Bisacchi GS, Saunders OL, Hafeez N, Miao W, Kapeller R, Zaller DM, Sali A, Weichenrieder O, Burns KH, Götte M, Rout MP, Arnold E, Greenbaum BD, Romero DL, LaCava J, Taylor MS. PMID: 38096902; PMCID: PMC10830420.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    17. Multi-scale photocatalytic proximity labeling reveals cell surface neighbors on and between cells. bioRxiv. 2023 Oct 29. Lin Z, Schaefer K, Lui I, Yao Z, Fossati A, Swaney DL, Palar A, Sali A, Wells JA. PMID: 37961561; PMCID: PMC10634877.
      View in: PubMed   Mentions: 1  
    18. Implications of a multiscale structure of the yeast nuclear pore complex. Mol Cell. 2023 09 21; 83(18):3283-3302.e5. Akey CW, Echeverria I, Ouch C, Nudelman I, Shi Y, Wang J, Chait BT, Sali A, Fernandez-Martinez J, Rout MP. PMID: 37738963; PMCID: PMC10630966.
      View in: PubMed   Mentions: 5     Fields:    Translation:AnimalsCells
    19. Illuminating the Function of the Orphan Transporter, SLC22A10 in Humans and Other Primates. Res Sq. 2023 Sep 14. Yee SW, Ferrández-Peral L, Alentorn P, Fontsere C, Ceylan M, Koleske ML, Handin N, Artegoitia VM, Lara G, Chien HC, Zhou X, Dainat J, Zalevsky A, Sali A, Brand CM, Capra JA, Artursson P, Newman JW, Marques-Bonet T, Giacomini KM. PMID: 37790518; PMCID: PMC10543398.
      View in: PubMed   Mentions:
    20. Illuminating the Function of the Orphan Transporter, SLC22A10 in Humans and Other Primates. bioRxiv. 2023 Aug 12. Yee SW, Ferrández-Peral L, Alentorn P, Fontsere C, Ceylan M, Koleske ML, Handin N, Artegoitia VM, Lara G, Chien HC, Zhou X, Dainat J, Zalevsky A, Sali A, Brand CM, Capra JA, Artursson P, Newman JW, Marques-Bonet T, Giacomini KM. PMID: 37609337; PMCID: PMC10441401.
      View in: PubMed   Mentions:
    21. Soft X-ray Tomography for Mapping and Quantifying Intracellular Organelle Interactions. Microsc Microanal. 2023 Jul 22; 29(Supplement_1):1181. Loconte V, Singla J, Li A, Chen JH, Ekman A, McDermott G, Sali A, Gros ML, White KL, Larabell CA. PMID: 37613466.
      View in: PubMed   Mentions:    Fields:    
    22. Conformational Dynamics of the Activated GLP-1 Receptor-Gs Complex Revealed by Cross-Linking Mass Spectrometry and Integrative Structure Modeling. ACS Cent Sci. 2023 May 24; 9(5):992-1007. Yuan S, Xia L, Wang C, Wu F, Zhang B, Pan C, Fan Z, Lei X, Stevens RC, Sali A, Sun L, Shui W. PMID: 37252352; PMCID: PMC10214531.
      View in: PubMed   Mentions: 2  
    23. Dynamic molecular mechanism of the nuclear pore complex permeability barrier. bioRxiv. 2023 Apr 14. Kozai T, Fernandez-Martinez J, van Eeuwen T, Gallardo P, Kapinos LE, Mazur A, Zhang W, Tempkin J, Panatala R, Delgado-Izquierdo M, Raveh B, Sali A, Chait BT, Veenhoff LM, Rout MP, Lim RYH. PMID: 37066338; PMCID: PMC10103940.
      View in: PubMed   Mentions:
    24. In situ structure of actin remodeling during glucose-stimulated insulin secretion using cryo-electron tomography. Res Sq. 2023 Apr 04. Li W, Li A, Yu B, Zhang X, Liu X, White K, Stevens R, Baumeister W, Sali A, Jasnin M, Sun L. PMID: 37066286; PMCID: PMC10104243.
      View in: PubMed   Mentions:
    25. ModelCIF: An Extension of PDBx/mmCIF Data Representation for Computed Structure Models. J Mol Biol. 2023 07 15; 435(14):168021. Vallat B, Tauriello G, Bienert S, Haas J, Webb BM, Žídek A, Zheng W, Peisach E, Piehl DW, Anischanka I, Sillitoe I, Tolchard J, Varadi M, Baker D, Orengo C, Zhang Y, Hoch JC, Kurisu G, Patwardhan A, Velankar S, Burley SK, Sali A, Schwede T, Berman HM, Westbrook JD. PMID: 36828268; PMCID: PMC10293049.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    26. Structure and dynamics of the essential endogenous mycobacterial polyketide synthase Pks13. Nat Struct Mol Biol. 2023 03; 30(3):296-308. Kim SK, Dickinson MS, Finer-Moore J, Guan Z, Kaake RM, Echeverria I, Chen J, Pulido EH, Sali A, Krogan NJ, Rosenberg OS, Stroud RM. PMID: 36782050; PMCID: PMC10312659.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
    27. Structure and dynamics of the essential endogenous mycobacterial polyketide synthase Pks13. bioRxiv. 2023 Jan 28. Kim SK, Dickinson MS, Finer-Moore J, Guan Z, Kaake RM, Echeverria I, Chen J, Pulido EH, Sali A, Krogan NJ, Rosenberg OS, Stroud RM. PMID: 36747776; PMCID: PMC9900942.
      View in: PubMed   Mentions:
    28. RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning. Nucleic Acids Res. 2023 01 06; 51(D1):D488-D508. Burley SK, Bhikadiya C, Bi C, Bittrich S, Chao H, Chen L, Craig PA, Crichlow GV, Dalenberg K, Duarte JM, Dutta S, Fayazi M, Feng Z, Flatt JW, Ganesan S, Ghosh S, Goodsell DS, Green RK, Guranovic V, Henry J, Hudson BP, Khokhriakov I, Lawson CL, Liang Y, Lowe R, Peisach E, Persikova I, Piehl DW, Rose Y, Sali A, Segura J, Sekharan M, Shao C, Vallat B, Voigt M, Webb B, Westbrook JD, Whetstone S, Young JY, Zalevsky A, Zardecki C. PMID: 36420884; PMCID: PMC9825554.
      View in: PubMed   Mentions: 144     Fields:    Translation:Cells
    29. A quantitative map of nuclear pore assembly reveals two distinct mechanisms. Nature. 2023 01; 613(7944):575-581. Otsuka S, Tempkin JOB, Zhang W, Politi AZ, Rybina A, Hossain MJ, Kueblbeck M, Callegari A, Koch B, Morero NR, Sali A, Ellenberg J. PMID: 36599981; PMCID: PMC9849139.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansCells
    30. Electron microscopy holdings of the Protein Data Bank: the impact of the resolution revolution, new validation tools, and implications for the future. Biophys Rev. 2022 Dec; 14(6):1281-1301. Burley SK, Berman HM, Chiu W, Dai W, Flatt JW, Hudson BP, Kaelber JT, Khare SD, Kulczyk AW, Lawson CL, Pintilie GD, Sali A, Vallat B, Westbrook JD, Young JY, Zardecki C. PMID: 36474933; PMCID: PMC9715422.
      View in: PubMed   Mentions: 19  
    31. RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D. Protein Sci. 2022 12; 31(12):e4482. Burley SK, Bhikadiya C, Bi C, Bittrich S, Chao H, Chen L, Craig PA, Crichlow GV, Dalenberg K, Duarte JM, Dutta S, Fayazi M, Feng Z, Flatt JW, Ganesan SJ, Ghosh S, Goodsell DS, Green RK, Guranovic V, Henry J, Hudson BP, Khokhriakov I, Lawson CL, Liang Y, Lowe R, Peisach E, Persikova I, Piehl DW, Rose Y, Sali A, Segura J, Sekharan M, Shao C, Vallat B, Voigt M, Webb B, Westbrook JD, Whetstone S, Young JY, Zalevsky A, Zardecki C. PMID: 36281733; PMCID: PMC9667899.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansCells
    32. Protein Data Bank: A Comprehensive Review of 3D Structure Holdings and Worldwide Utilization by Researchers, Educators, and Students. Biomolecules. 2022 10 04; 12(10). Burley SK, Berman HM, Duarte JM, Feng Z, Flatt JW, Hudson BP, Lowe R, Peisach E, Piehl DW, Rose Y, Sali A, Sekharan M, Shao C, Vallat B, Voigt M, Westbrook JD, Young JY, Zardecki C. PMID: 36291635; PMCID: PMC9599165.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansCells
    33. An intensity-based post-processing tool for 3D instance segmentation of organelles in soft X-ray tomograms. PLoS One. 2022; 17(9):e0269887. Li A, Zhang S, Loconte V, Liu Y, Ekman A, Thompson GJ, Sali A, Stevens RC, White K, Singla J, Sun L. PMID: 36048824; PMCID: PMC9436087.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    34. Quantitative, in situ visualization of intracellular insulin vesicles in pancreatic beta cells. Proc Natl Acad Sci U S A. 2022 08 09; 119(32):e2202695119. Guo A, Zhang J, He B, Li A, Sun T, Li W, Wang J, Tai R, Liu Y, Qian Z, Fan J, Sali A, Stevens RC, Jiang H. PMID: 35921440; PMCID: PMC9371705.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCells
    35. Doublecortin engages the microtubule lattice through a cooperative binding mode involving its C-terminal domain. Elife. 2022 04 29; 11. Rafiei A, Cruz Tetlalmatzi S, Edrington CH, Lee L, Crowder DA, Saltzberg DJ, Sali A, Brouhard G, Schriemer DC. PMID: 35485925; PMCID: PMC9122500.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    36. Integrative structure determination of histones H3 and H4 using genetic interactions. FEBS J. 2023 05; 290(10):2565-2575. Echeverria I, Braberg H, Krogan NJ, Sali A. PMID: 35298864; PMCID: PMC9481981.
      View in: PubMed   Mentions: 1     Fields:    Translation:Animals
    37. The YΦ motif defines the structure-activity relationships of human 20S proteasome activators. Nat Commun. 2022 03 09; 13(1):1226. Opoku-Nsiah KA, de la Pena AH, Williams SK, Chopra N, Sali A, Lander GC, Gestwicki JE. PMID: 35264557; PMCID: PMC8907193.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    38. Soft X-ray tomography to map and quantify organelle interactions at the mesoscale. Structure. 2022 04 07; 30(4):510-521.e3. Loconte V, Singla J, Li A, Chen JH, Ekman A, McDermott G, Sali A, Le Gros M, White KL, Larabell CA. PMID: 35148829; PMCID: PMC9013509.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    39. Integration of software tools for integrative modeling of biomolecular systems. J Struct Biol. 2022 03; 214(1):107841. Hancock M, Peulen TO, Webb B, Poon B, Fraser JS, Adams P, Sali A. PMID: 35149213; PMCID: PMC9278553.
      View in: PubMed   Mentions: 5     Fields:    
    40. Soluble TREM2 inhibits secondary nucleation of Aβ fibrillization and enhances cellular uptake of fibrillar Aβ. Proc Natl Acad Sci U S A. 2022 02 01; 119(5). Belsare KD, Wu H, Mondal D, Bond A, Castillo E, Jin J, Jo H, Roush AE, Pilla KB, Sali A, Condello C, DeGrado WF. PMID: 35082148; PMCID: PMC8812518.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansAnimalsCells
    41. From systems to structure - using genetic data to model protein structures. Nat Rev Genet. 2022 06; 23(6):342-354. Braberg H, Echeverria I, Kaake RM, Sali A, Krogan NJ. PMID: 35013567; PMCID: PMC8744059.
      View in: PubMed   Mentions: 11     Fields:    
    42. Comprehensive structure and functional adaptations of the yeast nuclear pore complex. Cell. 2022 01 20; 185(2):361-378.e25. Akey CW, Singh D, Ouch C, Echeverria I, Nudelman I, Varberg JM, Yu Z, Fang F, Shi Y, Wang J, Salzberg D, Song K, Xu C, Gumbart JC, Suslov S, Unruh J, Jaspersen SL, Chait BT, Sali A, Fernandez-Martinez J, Ludtke SJ, Villa E, Rout MP. PMID: 34982960; PMCID: PMC8928745.
      View in: PubMed   Mentions: 63     Fields:    Translation:AnimalsCells
    43. Highly synergistic combinations of nanobodies that target SARS-CoV-2 and are resistant to escape. Elife. 2021 12 07; 10. Mast FD, Fridy PC, Ketaren NE, Wang J, Jacobs EY, Olivier JP, Sanyal T, Molloy KR, Schmidt F, Rutkowska M, Weisblum Y, Rich LM, Vanderwall ER, Dambrauskas N, Vigdorovich V, Keegan S, Jiler JB, Stein ME, Olinares PDB, Herlands L, Hatziioannou T, Sather DN, Debley JS, Fenyö D, Sali A, Bieniasz PD, Aitchison JD, Chait BT, Rout MP. PMID: 34874007; PMCID: PMC8651292.
      View in: PubMed   Mentions: 28     Fields:    Translation:HumansAnimalsCells
    44. New system for archiving integrative structures. Acta Crystallogr D Struct Biol. 2021 Dec 01; 77(Pt 12):1486-1496. Vallat B, Webb B, Fayazi M, Voinea S, Tangmunarunkit H, Ganesan SJ, Lawson CL, Westbrook JD, Kesselman C, Sali A, Berman HM. PMID: 34866606; PMCID: PMC8647179.
      View in: PubMed   Mentions: 18  Translation:Cells
    45. Reversible phosphorylation of cyclin T1 promotes assembly and stability of P-TEFb. Elife. 2021 11 25; 10. Huang F, Nguyen TT, Echeverria I, Rakesh R, Cary DC, Paculova H, Sali A, Weiss A, Peterlin BM, Fujinaga K. PMID: 34821217; PMCID: PMC8648303.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    46. RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D. Protein Sci. 2022 01; 31(1):187-208. Burley SK, Bhikadiya C, Bi C, Bittrich S, Chen L, Crichlow GV, Duarte JM, Dutta S, Fayazi M, Feng Z, Flatt JW, Ganesan SJ, Goodsell DS, Ghosh S, Kramer Green R, Guranovic V, Henry J, Hudson BP, Lawson CL, Liang Y, Lowe R, Peisach E, Persikova I, Piehl DW, Rose Y, Sali A, Segura J, Sekharan M, Shao C, Vallat B, Voigt M, Westbrook JD, Whetstone S, Young JY, Zardecki C. PMID: 34676613; PMCID: PMC8740825.
      View in: PubMed   Mentions: 53     Fields:    
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    93. 2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update. Acta Crystallogr D Struct Biol. 2017 Sep 01; 73(Pt 9):710-728. Trewhella J, Duff AP, Durand D, Gabel F, Guss JM, Hendrickson WA, Hura GL, Jacques DA, Kirby NM, Kwan AH, Pérez J, Pollack L, Ryan TM, Sali A, Schneidman-Duhovny D, Schwede T, Svergun DI, Sugiyama M, Tainer JA, Vachette P, Westbrook J, Whitten AE. PMID: 28876235; PMCID: PMC5586245.
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    94. The molecular architecture of the yeast spindle pole body core determined by Bayesian integrative modeling. Mol Biol Cell. 2017 Nov 07; 28(23):3298-3314. Viswanath S, Bonomi M, Kim SJ, Klenchin VA, Taylor KC, Yabut KC, Umbreit NT, Van Epps HA, Meehl J, Jones MH, Russel D, Velazquez-Muriel JA, Winey M, Rayment I, Davis TN, Sali A, Muller EG. PMID: 28814505; PMCID: PMC5687031.
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    95. The proteasome-interacting Ecm29 protein disassembles the 26S proteasome in response to oxidative stress. J Biol Chem. 2017 09 29; 292(39):16310-16320. Wang X, Chemmama IE, Yu C, Huszagh A, Xu Y, Viner R, Block SA, Cimermancic P, Rychnovsky SD, Ye Y, Sali A, Huang L. PMID: 28821611; PMCID: PMC5625060.
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    96. Human Concentrative Nucleoside Transporter 3 (hCNT3, SLC28A3) Forms a Cyclic Homotrimer. Biochemistry. 2017 07 11; 56(27):3475-3483. Stecula A, Schlessinger A, Giacomini KM, Sali A. PMID: 28661652; PMCID: PMC6917504.
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    97. Computational Discovery and Experimental Validation of Inhibitors of the Human Intestinal Transporter OATP2B1. J Chem Inf Model. 2017 06 26; 57(6):1402-1413. Khuri N, Zur AA, Wittwer MB, Lin L, Yee SW, Sali A, Giacomini KM. PMID: 28562037.
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    98. Regulation of Rvb1/Rvb2 by a Domain within the INO80 Chromatin Remodeling Complex Implicates the Yeast Rvbs as Protein Assembly Chaperones. Cell Rep. 2017 06 06; 19(10):2033-2044. Zhou CY, Stoddard CI, Johnston JB, Trnka MJ, Echeverria I, Palovcak E, Sali A, Burlingame AL, Cheng Y, Narlikar GJ. PMID: 28591576; PMCID: PMC5564220.
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    99. Reconstruction of 3D structures of MET antibodies from electron microscopy 2D class averages. PLoS One. 2017; 12(4):e0175758. Chen Q, Vieth M, Timm DE, Humblet C, Schneidman-Duhovny D, Chemmama IE, Sali A, Zeng W, Lu J, Liu L. PMID: 28406969; PMCID: PMC5391116.
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    100. Discovery of Competitive and Noncompetitive Ligands of the Organic Cation Transporter 1 (OCT1; SLC22A1). J Med Chem. 2017 04 13; 60(7):2685-2696. Chen EC, Khuri N, Liang X, Stecula A, Chien HC, Yee SW, Huang Y, Sali A, Giacomini KM. PMID: 28230985.
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    101. Molecular Details Underlying Dynamic Structures and Regulation of the Human 26S Proteasome. Mol Cell Proteomics. 2017 05; 16(5):840-854. Wang X, Cimermancic P, Yu C, Schweitzer A, Chopra N, Engel JL, Greenberg C, Huszagh AS, Beck F, Sakata E, Yang Y, Novitsky EJ, Leitner A, Nanni P, Kahraman A, Guo X, Dixon JE, Rychnovsky SD, Aebersold R, Baumeister W, Sali A, Huang L. PMID: 28292943; PMCID: PMC5417825.
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    102. Lineage-specific proteins essential for endocytosis in trypanosomes. J Cell Sci. 2017 04 15; 130(8):1379-1392. Manna PT, Obado SO, Boehm C, Gadelha C, Sali A, Chait BT, Rout MP, Field MC. PMID: 28232524; PMCID: PMC5399782.
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    103. Molecular Architecture of the Major Membrane Ring Component of the Nuclear Pore Complex. Structure. 2017 03 07; 25(3):434-445. Upla P, Kim SJ, Sampathkumar P, Dutta K, Cahill SM, Chemmama IE, Williams R, Bonanno JB, Rice WJ, Stokes DL, Cowburn D, Almo SC, Sali A, Rout MP, Fernandez-Martinez J. PMID: 28162953; PMCID: PMC5342941.
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    104. Protein Structure Modeling with MODELLER. Methods Mol Biol. 2017; 1654:39-54. Webb B, Sali A. PMID: 28986782.
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    105. A Residue-Resolved Bayesian Approach to Quantitative Interpretation of Hydrogen-Deuterium Exchange from Mass Spectrometry: Application to Characterizing Protein-Ligand Interactions. J Phys Chem B. 2017 04 20; 121(15):3493-3501. Saltzberg DJ, Broughton HB, Pellarin R, Chalmers MJ, Espada A, Dodge JA, Pascal BD, Griffin PR, Humblet C, Sali A. PMID: 27807976; PMCID: PMC5693600.
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    106. Editorial overview: Biophysical and molecular biological methods. Curr Opin Struct Biol. 2016 10; 40:ix-xi. Fromme P, Sali A. PMID: 27908508.
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    107. Clustering of disulfide-rich peptides provides scaffolds for hit discovery by phage display: application to interleukin-23. BMC Bioinformatics. 2016 Nov 23; 17(1):481. Barkan DT, Cheng XL, Celino H, Tran TT, Bhandari A, Craik CS, Sali A, Smythe ML. PMID: 27881076; PMCID: PMC5120537.
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    108. Structure and Function of the Nuclear Pore Complex Cytoplasmic mRNA Export Platform. Cell. 2016 11 17; 167(5):1215-1228.e25. Fernandez-Martinez J, Kim SJ, Shi Y, Upla P, Pellarin R, Gagnon M, Chemmama IE, Wang J, Nudelman I, Zhang W, Williams R, Rice WJ, Stokes DL, Zenklusen D, Chait BT, Sali A, Rout MP. PMID: 27839866; PMCID: PMC5130164.
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    109. Comparative Protein Structure Modeling Using MODELLER. Curr Protoc Protein Sci. 2016 Nov 01; 86:2.9.1-2.9.37. Webb B, Sali A. PMID: 27801516.
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    110. Guinea Pig Prion Protein Supports Rapid Propagation of Bovine Spongiform Encephalopathy and Variant Creutzfeldt-Jakob Disease Prions. J Virol. 2016 11 01; 90(21):9558-9569. Watts JC, Giles K, Saltzberg DJ, Dugger BN, Patel S, Oehler A, Bhardwaj S, Sali A, Prusiner SB. PMID: 27440899; PMCID: PMC5068510.
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    111. Insights into HIV-1 proviral transcription from integrative structure and dynamics of the Tat:AFF4:P-TEFb:TAR complex. Elife. 2016 10 12; 5. Schulze-Gahmen U, Echeverria I, Stjepanovic G, Bai Y, Lu H, Schneidman-Duhovny D, Doudna JA, Zhou Q, Sali A, Hurley JH. PMID: 27731797; PMCID: PMC5072841.
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    112. Simple rules for passive diffusion through the nuclear pore complex. J Cell Biol. 2016 Oct 10; 215(1):57-76. Timney BL, Raveh B, Mironska R, Trivedi JM, Kim SJ, Russel D, Wente SR, Sali A, Rout MP. PMID: 27697925; PMCID: PMC5057280.
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    113. Comparative Protein Structure Modeling Using MODELLER. Curr Protoc Bioinformatics. 2016 06 20; 54:5.6.1-5.6.37. Webb B, Sali A. PMID: 27322406; PMCID: PMC5031415.
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    114. Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment. Proteins. 2016 09; 84 Suppl 1:323-48. Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, Park S, Heo L, Rie Lee G, Seok C, Qin S, Zhou HX, Ritchie DW, Maigret B, Devignes MD, Ghoorah A, Torchala M, Chaleil RA, Bates PA, Ben-Zeev E, Eisenstein M, Negi SS, Weng Z, Vreven T, Pierce BG, Borrman TM, Yu J, Ochsenbein F, Guerois R, Vangone A, Rodrigues JP, van Zundert G, Nellen M, Xue L, Karaca E, Melquiond AS, Visscher K, Kastritis PL, Bonvin AM, Xu X, Qiu L, Yan C, Li J, Ma Z, Cheng J, Zou X, Shen Y, Peterson LX, Kim HR, Roy A, Han X, Esquivel-Rodriguez J, Kihara D, Yu X, Bruce NJ, Fuller JC, Wade RC, Anishchenko I, Kundrotas PJ, Vakser IA, Imai K, Yamada K, Oda T, Nakamura T, Tomii K, Pallara C, Romero-Durana M, Jiménez-García B, Moal IH, Férnandez-Recio J, Joung JY, Kim JY, Joo K, Lee J, Kozakov D, Vajda S, Mottarella S, Hall DR, Beglov D, Mamonov A, Xia B, Bohnuud T, Del Carpio CA, Ichiishi E, Marze N, Kuroda D, Roy Burman SS, Gray JJ, Chermak E, Cavallo L, Oliva R, Tovchigrechko A, Wodak SJ. PMID: 27122118; PMCID: PMC5030136.
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    115. Structure of Complement C3(H2O) Revealed By Quantitative Cross-Linking/Mass Spectrometry And Modeling. Mol Cell Proteomics. 2016 08; 15(8):2730-43. Chen ZA, Pellarin R, Fischer L, Sali A, Nilges M, Barlow PN, Rappsilber J. PMID: 27250206; PMCID: PMC4974347.
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    116. FoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles. Nucleic Acids Res. 2016 Jul 08; 44(W1):W424-9. Schneidman-Duhovny D, Hammel M, Tainer JA, Sali A. PMID: 27151198; PMCID: PMC4987932.
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    117. Slide-and-exchange mechanism for rapid and selective transport through the nuclear pore complex. Proc Natl Acad Sci U S A. 2016 May 03; 113(18):E2489-97. Raveh B, Karp JM, Sparks S, Dutta K, Rout MP, Sali A, Cowburn D. PMID: 27091992; PMCID: PMC4983827.
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    118. A phosphotyrosine switch regulates organic cation transporters. Nat Commun. 2016 Mar 16; 7:10880. Sprowl JA, Ong SS, Gibson AA, Hu S, Du G, Lin W, Li L, Bharill S, Ness RA, Stecula A, Offer SM, Diasio RB, Nies AT, Schwab M, Cavaletti G, Schlatter E, Ciarimboli G, Schellens JHM, Isacoff EY, Sali A, Chen T, Baker SD, Sparreboom A, Pabla N. PMID: 26979622; PMCID: PMC4799362.
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    119. Structure of γ-tubulin small complex based on a cryo-EM map, chemical cross-links, and a remotely related structure. J Struct Biol. 2016 06; 194(3):303-10. Greenberg CH, Kollman J, Zelter A, Johnson R, MacCoss MJ, Davis TN, Agard DA, Sali A. PMID: 26968363; PMCID: PMC4866596.
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    120. CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites. J Mol Biol. 2016 Feb 22; 428(4):709-719. Cimermancic P, Weinkam P, Rettenmaier TJ, Bichmann L, Keedy DA, Woldeyes RA, Schneidman-Duhovny D, Demerdash ON, Mitchell JC, Wells JA, Fraser JS, Sali A. PMID: 26854760; PMCID: PMC4794384.
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    121. Novel TKI-resistant BCR-ABL1 gatekeeper residue mutations retain in vitro sensitivity to axitinib. Leukemia. 2016 06; 30(6):1405-9. Lasater EA, Massi ES, Stecula A, Politi J, Tan SK, Smith CC, Gunthorpe M, Holmes JP, Chehab F, Sali A, Shah NP. PMID: 26511402.
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    122. Assembly and Molecular Architecture of the Phosphoinositide 3-Kinase p85α Homodimer. J Biol Chem. 2015 Dec 18; 290(51):30390-405. LoPiccolo J, Kim SJ, Shi Y, Wu B, Wu H, Chait BT, Singer RH, Sali A, Brenowitz M, Bresnick AR, Backer JM. PMID: 26475863; PMCID: PMC4683262.
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    123. Small-Molecule Allosteric Modulators of the Protein Kinase PDK1 from Structure-Based Docking. J Med Chem. 2015 Oct 22; 58(20):8285-8291. Rettenmaier TJ, Fan H, Karpiak J, Doak A, Sali A, Shoichet BK, Wells JA. PMID: 26443011; PMCID: PMC5099076.
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    124. A strategy for dissecting the architectures of native macromolecular assemblies. Nat Methods. 2015 Dec; 12(12):1135-8. Shi Y, Pellarin R, Fridy PC, Fernandez-Martinez J, Thompson MK, Li Y, Wang QJ, Sali A, Rout MP, Chait BT. PMID: 26436480; PMCID: PMC4803312.
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    125. Molecular architecture of the yeast Mediator complex. Elife. 2015 Sep 24; 4. Robinson PJ, Trnka MJ, Pellarin R, Greenberg CH, Bushnell DA, Davis R, Burlingame AL, Sali A, Kornberg RD. PMID: 26402457; PMCID: PMC4631838.
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    126. Architecture of the Human and Yeast General Transcription and DNA Repair Factor TFIIH. Mol Cell. 2015 Sep 03; 59(5):794-806. Luo J, Cimermancic P, Viswanath S, Ebmeier CC, Kim B, Dehecq M, Raman V, Greenberg CH, Pellarin R, Sali A, Taatjes DJ, Hahn S, Ranish J. PMID: 26340423; PMCID: PMC4560838.
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    127. Prediction of Functionally Important Phospho-Regulatory Events in Xenopus laevis Oocytes. PLoS Comput Biol. 2015 Aug; 11(8):e1004362. Johnson JR, Santos SD, Johnson T, Pieper U, Strumillo M, Wagih O, Sali A, Krogan NJ, Beltrao P. PMID: 26312481; PMCID: PMC4552029.
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    128. Structural Model of the Bilitranslocase Transmembrane Domain Supported by NMR and FRET Data. PLoS One. 2015; 10(8):e0135455. Roy Choudhury A, Sikorska E, van den Boom J, Bayer P, Popenda L, Szutkowski K, Jurga S, Bonomi M, Sali A, Zhukov I, Passamonti S, Novic M. PMID: 26291722; PMCID: PMC4546402.
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    129. Prion Protein-Antibody Complexes Characterized by Chromatography-Coupled Small-Angle X-Ray Scattering. Biophys J. 2015 Aug 18; 109(4):793-805. Carter L, Kim SJ, Schneidman-Duhovny D, Stöhr J, Poncet-Montange G, Weiss TM, Tsuruta H, Prusiner SB, Sali A. PMID: 26287631; PMCID: PMC4547163.
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    130. FLT3 D835 mutations confer differential resistance to type II FLT3 inhibitors. Leukemia. 2015 Dec; 29(12):2390-2. Smith CC, Lin K, Stecula A, Sali A, Shah NP. PMID: 26108694; PMCID: PMC4675689.
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    131. Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. Structure. 2015 Jul 07; 23(7):1156-67. Sali A, Berman HM, Schwede T, Trewhella J, Kleywegt G, Burley SK, Markley J, Nakamura H, Adams P, Bonvin AM, Chiu W, Peraro MD, Di Maio F, Ferrin TE, Grünewald K, Gutmanas A, Henderson R, Hummer G, Iwasaki K, Johnson G, Lawson CL, Meiler J, Marti-Renom MA, Montelione GT, Nilges M, Nussinov R, Patwardhan A, Rappsilber J, Read RJ, Saibil H, Schröder GF, Schwieters CD, Seidel CA, Svergun D, Topf M, Ulrich EL, Velankar S, Westbrook JD. PMID: 26095030; PMCID: PMC4933300.
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    132. Growing an editorial board for an ever expanding field. Structure. 2015 Apr 07; 23(4):605. Lima CD, Sali A, Kostic M. PMID: 25862929.
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    133. Scoring Large-Scale Affinity Purification Mass Spectrometry Datasets with MiST. Curr Protoc Bioinformatics. 2015 Mar 09; 49:8.19.1-8.19.16. Verschueren E, Von Dollen J, Cimermancic P, Gulbahce N, Sali A, Krogan NJ. PMID: 25754993; PMCID: PMC4378866.
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    134. Ring closure activates yeast γTuRC for species-specific microtubule nucleation. Nat Struct Mol Biol. 2015 Feb; 22(2):132-7. Kollman JM, Greenberg CH, Li S, Moritz M, Zelter A, Fong KK, Fernandez JJ, Sali A, Kilmartin J, Davis TN, Agard DA. PMID: 25599398; PMCID: PMC4318760.
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    135. Topological models of heteromeric protein assemblies from mass spectrometry: application to the yeast eIF3:eIF5 complex. Chem Biol. 2015 Jan 22; 22(1):117-28. Politis A, Schmidt C, Tjioe E, Sandercock AM, Lasker K, Gordiyenko Y, Russel D, Sali A, Robinson CV. PMID: 25544043; PMCID: PMC4306531.
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    136. A systematic computational analysis of biosynthetic gene cluster evolution: lessons for engineering biosynthesis. PLoS Comput Biol. 2014 Dec; 10(12):e1004016. Medema MH, Cimermancic P, Sali A, Takano E, Fischbach MA. PMID: 25474254; PMCID: PMC4256081.
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    137. Molecular Architecture of the 40S⋅eIF1⋅eIF3 Translation Initiation Complex. Cell. 2014 Nov 20; 159(5):1227-1228. Erzberger JP, Stengel F, Pellarin R, Zhang S, Schaefer T, Aylett CHS, Cimermancic P, Boehringer D, Sali A, Aebersold R, Ban N. PMID: 28898626; PMCID: PMC5628955.
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    139. Uncertainty in integrative structural modeling. Curr Opin Struct Biol. 2014 Oct; 28:96-104. Schneidman-Duhovny D, Pellarin R, Sali A. PMID: 25173450; PMCID: PMC4252396.
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    140. Molecular architecture of the 40S⋅eIF1⋅eIF3 translation initiation complex. Cell. 2014 08 28; 158(5):1123-1135. Erzberger JP, Stengel F, Pellarin R, Zhang S, Schaefer T, Aylett CHS, Cimermancic P, Boehringer D, Sali A, Aebersold R, Ban N. PMID: 25171412; PMCID: PMC4151992.
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    141. Structural characterization by cross-linking reveals the detailed architecture of a coatomer-related heptameric module from the nuclear pore complex. Mol Cell Proteomics. 2014 Nov; 13(11):2927-43. Shi Y, Fernandez-Martinez J, Tjioe E, Pellarin R, Kim SJ, Williams R, Schneidman-Duhovny D, Sali A, Rout MP, Chait BT. PMID: 25161197; PMCID: PMC4223482.
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    142. Molecular architecture of photoreceptor phosphodiesterase elucidated by chemical cross-linking and integrative modeling. J Mol Biol. 2014 Nov 11; 426(22):3713-3728. Zeng-Elmore X, Gao XZ, Pellarin R, Schneidman-Duhovny D, Zhang XJ, Kozacka KA, Tang Y, Sali A, Chalkley RJ, Cote RH, Chu F. PMID: 25149264; PMCID: PMC4253074.
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    143. Determining protein complex structures based on a Bayesian model of in vivo Förster resonance energy transfer (FRET) data. Mol Cell Proteomics. 2014 Nov; 13(11):2812-23. Bonomi M, Pellarin R, Kim SJ, Russel D, Sundin BA, Riffle M, Jaschob D, Ramsden R, Davis TN, Muller EG, Sali A. PMID: 25139910; PMCID: PMC4223474.
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    144. Integrative structure-function mapping of the nucleoporin Nup133 suggests a conserved mechanism for membrane anchoring of the nuclear pore complex. Mol Cell Proteomics. 2014 Nov; 13(11):2911-26. Kim SJ, Fernandez-Martinez J, Sampathkumar P, Martel A, Matsui T, Tsuruta H, Weiss TM, Shi Y, Markina-Inarrairaegui A, Bonanno JB, Sauder JM, Burley SK, Chait BT, Almo SC, Rout MP, Sali A. PMID: 25139911; PMCID: PMC4223481.
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    145. Cys-scanning disulfide crosslinking and bayesian modeling probe the transmembrane signaling mechanism of the histidine kinase, PhoQ. Structure. 2014 Sep 02; 22(9):1239-1251. Molnar KS, Bonomi M, Pellarin R, Clinthorne GD, Gonzalez G, Goldberg SD, Goulian M, Sali A, DeGrado WF. PMID: 25087511; PMCID: PMC4322757.
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    146. Molecular architecture and function of the SEA complex, a modulator of the TORC1 pathway. Mol Cell Proteomics. 2014 Nov; 13(11):2855-70. Algret R, Fernandez-Martinez J, Shi Y, Kim SJ, Pellarin R, Cimermancic P, Cochet E, Sali A, Chait BT, Rout MP, Dokudovskaya S. PMID: 25073740; PMCID: PMC4223477.
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    147. Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters. Cell. 2014 Jul 17; 158(2):412-421. Cimermancic P, Medema MH, Claesen J, Kurita K, Wieland Brown LC, Mavrommatis K, Pati A, Godfrey PA, Koehrsen M, Clardy J, Birren BW, Takano E, Sali A, Linington RG, Fischbach MA. PMID: 25036635; PMCID: PMC4123684.
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    148. Prediction of substrates for glutathione transferases by covalent docking. J Chem Inf Model. 2014 Jun 23; 54(6):1687-99. Dong GQ, Calhoun S, Fan H, Kalyanaraman C, Branch MC, Mashiyama ST, London N, Jacobson MP, Babbitt PC, Shoichet BK, Armstrong RN, Sali A. PMID: 24802635; PMCID: PMC4068255.
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    149. Elucidating the mechanism of substrate recognition by the bacterial Hsp90 molecular chaperone. J Mol Biol. 2014 Jun 12; 426(12):2393-404. Street TO, Zeng X, Pellarin R, Bonomi M, Sali A, Kelly MJ, Chu F, Agard DA. PMID: 24726919; PMCID: PMC5322795.
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    150. Protein structure modeling with MODELLER. Methods Mol Biol. 2014; 1137:1-15. Webb B, Sali A. PMID: 24573470.
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    151. Modeling of proteins and their assemblies with the Integrative Modeling Platform. Methods Mol Biol. 2014; 1091:277-95. Webb B, Lasker K, Velázquez-Muriel J, Schneidman-Duhovny D, Pellarin R, Bonomi M, Greenberg C, Raveh B, Tjioe E, Russel D, Sali A. PMID: 24203340.
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    152. SAXS Merge: an automated statistical method to merge SAXS profiles using Gaussian processes. J Synchrotron Radiat. 2014 Jan; 21(Pt 1):203-8. Spill YG, Kim SJ, Schneidman-Duhovny D, Russel D, Webb B, Sali A, Nilges M. PMID: 24365937; PMCID: PMC3874021.
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    153. ModBase, a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res. 2014 Jan; 42(Database issue):D336-46. Pieper U, Webb BM, Dong GQ, Schneidman-Duhovny D, Fan H, Kim SJ, Khuri N, Spill YG, Weinkam P, Hammel M, Tainer JA, Nilges M, Sali A. PMID: 24271400; PMCID: PMC3965011.
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    154. High-resolution network biology: connecting sequence with function. Nat Rev Genet. 2013 Dec; 14(12):865-79. Ryan CJ, Cimermancic P, Szpiech ZA, Sali A, Hernandez RD, Krogan NJ. PMID: 24197012; PMCID: PMC4023809.
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    155. Recovering a representative conformational ensemble from underdetermined macromolecular structural data. J Am Chem Soc. 2013 Nov 06; 135(44):16595-609. Berlin K, Castañeda CA, Schneidman-Duhovny D, Sali A, Nava-Tudela A, Fushman D. PMID: 24093873; PMCID: PMC3902174.
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    156. Target prediction for an open access set of compounds active against Mycobacterium tuberculosis. PLoS Comput Biol. 2013; 9(10):e1003253. Martínez-Jiménez F, Papadatos G, Yang L, Wallace IM, Kumar V, Pieper U, Sali A, Brown JR, Overington JP, Marti-Renom MA. PMID: 24098102; PMCID: PMC3789770.
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    157. Optimized atomic statistical potentials: assessment of protein interfaces and loops. Bioinformatics. 2013 Dec 15; 29(24):3158-66. Dong GQ, Fan H, Schneidman-Duhovny D, Webb B, Sali A. PMID: 24078704; PMCID: PMC3842762.
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    158. Mapping polymerization and allostery of hemoglobin S using point mutations. J Phys Chem B. 2013 Oct 24; 117(42):13058-68. Weinkam P, Sali A. PMID: 23957820; PMCID: PMC3973026.
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    159. Structure-guided discovery of new deaminase enzymes. J Am Chem Soc. 2013 Sep 18; 135(37):13927-33. Hitchcock DS, Fan H, Kim J, Vetting M, Hillerich B, Seidel RD, Almo SC, Shoichet BK, Sali A, Raushel FM. PMID: 23968233; PMCID: PMC3827683.
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    160. Deamination of 6-aminodeoxyfutalosine in menaquinone biosynthesis by distantly related enzymes. Biochemistry. 2013 Sep 17; 52(37):6525-36. Goble AM, Toro R, Li X, Ornelas A, Fan H, Eswaramoorthy S, Patskovsky Y, Hillerich B, Seidel R, Sali A, Shoichet BK, Almo SC, Swaminathan S, Tanner ME, Raushel FM. PMID: 23972005; PMCID: PMC3813303.
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    161. Celebrating 20 years of Structure. Structure. 2013 Sep 03; 21(9):1477-8. Lima CD, Sali A, Kostic M. PMID: 24010704.
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    162. Accurate SAXS profile computation and its assessment by contrast variation experiments. Biophys J. 2013 Aug 20; 105(4):962-74. Schneidman-Duhovny D, Hammel M, Tainer JA, Sali A. PMID: 23972848; PMCID: PMC3752106.
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    163. Consequences of domain insertion on sequence-structure divergence in a superfold. Proc Natl Acad Sci U S A. 2013 Sep 03; 110(36):E3381-7. Pandya C, Brown S, Pieper U, Sali A, Dunaway-Mariano D, Babbitt PC, Xia Y, Allen KN. PMID: 23959887; PMCID: PMC3767544.
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    164. Report of the wwPDB Small-Angle Scattering Task Force: data requirements for biomolecular modeling and the PDB. Structure. 2013 Jun 04; 21(6):875-81. Trewhella J, Hendrickson WA, Kleywegt GJ, Sali A, Sato M, Schwede T, Svergun DI, Tainer JA, Westbrook J, Berman HM. PMID: 23747111.
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    165. Structural basis for alternating access of a eukaryotic calcium/proton exchanger. Nature. 2013 Jul 04; 499(7456):107-10. Waight AB, Pedersen BP, Schlessinger A, Bonomi M, Chau BH, Roe-Zurz Z, Risenmay AJ, Sali A, Stroud RM. PMID: 23685453; PMCID: PMC3702627.
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    166. Evolution of modular intraflagellar transport from a coatomer-like progenitor. Proc Natl Acad Sci U S A. 2013 Apr 23; 110(17):6943-8. van Dam TJ, Townsend MJ, Turk M, Schlessinger A, Sali A, Field MC, Huynen MA. PMID: 23569277; PMCID: PMC3637775.
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    167. Crystal structure of a eukaryotic phosphate transporter. Nature. 2013 Apr 25; 496(7446):533-6. Pedersen BP, Kumar H, Waight AB, Risenmay AJ, Roe-Zurz Z, Chau BH, Schlessinger A, Bonomi M, Harries W, Sali A, Johri AK, Stroud RM. PMID: 23542591; PMCID: PMC3678552.
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    168. Structure-based ligand discovery for the Large-neutral Amino Acid Transporter 1, LAT-1. Proc Natl Acad Sci U S A. 2013 Apr 02; 110(14):5480-5. Geier EG, Schlessinger A, Fan H, Gable JE, Irwin JJ, Sali A, Giacomini KM. PMID: 23509259; PMCID: PMC3619328.
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    169. Structure, dynamics, evolution, and function of a major scaffold component in the nuclear pore complex. Structure. 2013 Apr 02; 21(4):560-71. Sampathkumar P, Kim SJ, Upla P, Rice WJ, Phillips J, Timney BL, Pieper U, Bonanno JB, Fernandez-Martinez J, Hakhverdyan Z, Ketaren NE, Matsui T, Weiss TM, Stokes DL, Sauder JM, Burley SK, Sali A, Rout MP, Almo SC. PMID: 23499021; PMCID: PMC3755625.
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    170. All-atom ensemble modeling to analyze small-angle x-ray scattering of glycosylated proteins. Structure. 2013 Mar 05; 21(3):321-31. Guttman M, Weinkam P, Sali A, Lee KK. PMID: 23473666; PMCID: PMC3840220.
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    171. Biochemistry. Integrative structural biology. Science. 2013 Feb 22; 339(6122):913-5. Ward AB, Sali A, Wilson IA. PMID: 23430643; PMCID: PMC3633482.
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    172. Coordinating the impact of structural genomics on the human α-helical transmembrane proteome. Nat Struct Mol Biol. 2013 Feb; 20(2):135-8. Pieper U, Schlessinger A, Kloppmann E, Chang GA, Chou JJ, Dumont ME, Fox BG, Fromme P, Hendrickson WA, Malkowski MG, Rees DC, Stokes DL, Stowell MH, Wiener MC, Rost B, Stroud RM, Stevens RC, Sali A. PMID: 23381628; PMCID: PMC3645303.
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    173. Discovery of potent, selective multidrug and toxin extrusion transporter 1 (MATE1, SLC47A1) inhibitors through prescription drug profiling and computational modeling. J Med Chem. 2013 Feb 14; 56(3):781-795. Wittwer MB, Zur AA, Khuri N, Kido Y, Kosaka A, Zhang X, Morrissey KM, Sali A, Huang Y, Giacomini KM. PMID: 23241029; PMCID: PMC4068829.
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    174. Assignment of pterin deaminase activity to an enzyme of unknown function guided by homology modeling and docking. J Am Chem Soc. 2013 Jan 16; 135(2):795-803. Fan H, Hitchcock DS, Seidel RD, Hillerich B, Lin H, Almo SC, Sali A, Shoichet BK, Raushel FM. PMID: 23256477; PMCID: PMC3557803.
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    175. Molecular modeling and ligand docking for solute carrier (SLC) transporters. Curr Top Med Chem. 2013; 13(7):843-56. Schlessinger A, Khuri N, Giacomini KM, Sali A. PMID: 23578028; PMCID: PMC4056341.
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    176. Impact of mutations on the allosteric conformational equilibrium. J Mol Biol. 2013 Feb 08; 425(3):647-61. Weinkam P, Chen YC, Pons J, Sali A. PMID: 23228330; PMCID: PMC3557769.
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    177. Limits of ligand selectivity from docking to models: in silico screening for A(1) adenosine receptor antagonists. PLoS One. 2012; 7(11):e49910. Kolb P, Phan K, Gao ZG, Marko AC, Sali A, Jacobson KA. PMID: 23185482; PMCID: PMC3503826.
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    178. Assembly of macromolecular complexes by satisfaction of spatial restraints from electron microscopy images. Proc Natl Acad Sci U S A. 2012 Nov 13; 109(46):18821-6. Velázquez-Muriel J, Lasker K, Russel D, Phillips J, Webb BM, Schneidman-Duhovny D, Sali A. PMID: 23112201; PMCID: PMC3503186.
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    179. A method for integrative structure determination of protein-protein complexes. Bioinformatics. 2012 Dec 15; 28(24):3282-9. Schneidman-Duhovny D, Rossi A, Avila-Sakar A, Kim SJ, Velázquez-Muriel J, Strop P, Liang H, Krukenberg KA, Liao M, Kim HM, Sobhanifar S, Dötsch V, Rajpal A, Pons J, Agard DA, Cheng Y, Sali A. PMID: 23093611; PMCID: PMC3519461.
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    180. Self-assembly of filamentous amelogenin requires calcium and phosphate: from dimers via nanoribbons to fibrils. Biomacromolecules. 2012 Nov 12; 13(11):3494-502. Martinez-Avila O, Wu S, Kim SJ, Cheng Y, Khan F, Samudrala R, Sali A, Horst JA, Habelitz S. PMID: 22974364; PMCID: PMC3496023.
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    181. In support of the BMRB. Nat Struct Mol Biol. 2012 Sep; 19(9):854-60. Markley JL, Akutsu H, Asakura T, Baldus M, Boelens R, Bonvin A, Kaptein R, Bax A, Bezsonova I, Gryk MR, Hoch JC, Korzhnev DM, Maciejewski MW, Case D, Chazin WJ, Cross TA, Dames S, Kessler H, Lange O, Madl T, Reif B, Sattler M, Eliezer D, Fersht A, Forman-Kay J, Kay LE, Fraser J, Gross J, Kortemme T, Sali A, Fujiwara T, Gardner K, Luo X, Rizo-Rey J, Rosen M, Gil RR, Ho C, Rule G, Gronenborn AM, Ishima R, Klein-Seetharaman J, Tang P, van der Wel P, Xu Y, Grzesiek S, Hiller S, Seelig J, Laue ED, Mott H, Nietlispach D, Barsukov I, Lian LY, Middleton D, Blumenschein T, Moore G, Campbell I, Schnell J, Vakonakis IJ, Watts A, Conte MR, Mason J, Pfuhl M, Sanderson MR, Craven J, Williamson M, Dominguez C, Roberts G, Günther U, Overduin M, Werner J, Williamson P, Blindauer C, Crump M, Driscoll P, Frenkiel T, Golovanov A, Matthews S, Parkinson J, Uhrin D, Williams M, Neuhaus D, Oschkinat H, Ramos A, Shaw DE, Steinbeck C, Vendruscolo M, Vuister GW, Walters KJ, Weinstein H, Wüthrich K, Yokoyama S. PMID: 22955930.
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    182. Strategic protein target analysis for developing drugs to stop dental caries. Adv Dent Res. 2012 Sep; 24(2):86-93. Horst JA, Pieper U, Sali A, Zhan L, Chopra G, Samudrala R, Featherstone JD. PMID: 22899687; PMCID: PMC3420364.
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    183. High selectivity of the γ-aminobutyric acid transporter 2 (GAT-2, SLC6A13) revealed by structure-based approach. J Biol Chem. 2012 Nov 02; 287(45):37745-56. Schlessinger A, Wittwer MB, Dahlin A, Khuri N, Bonomi M, Fan H, Giacomini KM, Sali A. PMID: 22932902; PMCID: PMC3488050.
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    184. Integrative structural modeling with small angle X-ray scattering profiles. BMC Struct Biol. 2012 Jul 16; 12:17. Schneidman-Duhovny D, Kim SJ, Sali A. PMID: 22800408; PMCID: PMC3427135.
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    185. Atomic structure of the nuclear pore complex targeting domain of a Nup116 homologue from the yeast, Candida glabrata. Proteins. 2012 Aug; 80(8):2110-6. Sampathkumar P, Kim SJ, Manglicmot D, Bain KT, Gilmore J, Gheyi T, Phillips J, Pieper U, Fernandez-Martinez J, Franke JD, Matsui T, Tsuruta H, Atwell S, Thompson DA, Emtage JS, Wasserman SR, Rout MP, Sali A, Sauder JM, Almo SC, Burley SK. PMID: 22544723; PMCID: PMC3686472.
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    186. Global identification and characterization of both O-GlcNAcylation and phosphorylation at the murine synapse. Mol Cell Proteomics. 2012 Aug; 11(8):215-29. Trinidad JC, Barkan DT, Gulledge BF, Thalhammer A, Sali A, Schoepfer R, Burlingame AL. PMID: 22645316; PMCID: PMC3412957.
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    187. SALIGN: a web server for alignment of multiple protein sequences and structures. Bioinformatics. 2012 Aug 01; 28(15):2072-3. Braberg H, Webb BM, Tjioe E, Pieper U, Sali A, Madhusudhan MS. PMID: 22618536; PMCID: PMC3400954.
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    188. Facile backbone structure determination of human membrane proteins by NMR spectroscopy. Nat Methods. 2012 May 20; 9(8):834-9. Klammt C, Maslennikov I, Bayrhuber M, Eichmann C, Vajpai N, Chiu EJ, Blain KY, Esquivies L, Kwon JH, Balana B, Pieper U, Sali A, Slesinger PA, Kwiatkowski W, Riek R, Choe S. PMID: 22609626; PMCID: PMC3723349.
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    189. Structure-based model of allostery predicts coupling between distant sites. Proc Natl Acad Sci U S A. 2012 Mar 27; 109(13):4875-80. Weinkam P, Pons J, Sali A. PMID: 22403063; PMCID: PMC3324024.
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    190. Biochemical characterization and structural modeling of human cathepsin E variant 2 in comparison to the wild-type protein. Biol Chem. 2012 Mar; 393(3):177-86. Puizdar V, Zajc T, Zerovnik E, Renko M, Pieper U, Eswar N, Sali A, Dolenc I, Turk V. PMID: 22718633; PMCID: PMC4111641.
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    191. Structure-function mapping of a heptameric module in the nuclear pore complex. J Cell Biol. 2012 Feb 20; 196(4):419-34. Fernandez-Martinez J, Phillips J, Sekedat MD, Diaz-Avalos R, Velazquez-Muriel J, Franke JD, Williams R, Stokes DL, Chait BT, Sali A, Rout MP. PMID: 22331846; PMCID: PMC3283990.
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    192. Outcome of the first electron microscopy validation task force meeting. Structure. 2012 Feb 08; 20(2):205-14. Henderson R, Sali A, Baker ML, Carragher B, Devkota B, Downing KH, Egelman EH, Feng Z, Frank J, Grigorieff N, Jiang W, Ludtke SJ, Medalia O, Penczek PA, Rosenthal PB, Rossmann MG, Schmid MF, Schröder GF, Steven AC, Stokes DL, Westbrook JD, Wriggers W, Yang H, Young J, Berman HM, Chiu W, Kleywegt GJ, Lawson CL. PMID: 22325770; PMCID: PMC3328769.
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    193. Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach. Proc Natl Acad Sci U S A. 2012 Jan 31; 109(5):1380-7. Lasker K, Förster F, Bohn S, Walzthoeni T, Villa E, Unverdorben P, Beck F, Aebersold R, Sali A, Baumeister W. PMID: 22307589; PMCID: PMC3277140.
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    195. Macromolecular assembly structures by comparative modeling and electron microscopy. Methods Mol Biol. 2012; 857:331-50. Lasker K, Velázquez-Muriel JA, Webb BM, Yang Z, Ferrin TE, Sali A. PMID: 22323229.
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    196. Virtual ligand screening against comparative protein structure models. Methods Mol Biol. 2012; 819:105-26. Fan H, Irwin JJ, Sali A. PMID: 22183533; PMCID: PMC3386294.
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    197. Vif hijacks CBF-β to degrade APOBEC3G and promote HIV-1 infection. Nature. 2011 Dec 21; 481(7381):371-5. Jäger S, Kim DY, Hultquist JF, Shindo K, LaRue RS, Kwon E, Li M, Anderson BD, Yen L, Stanley D, Mahon C, Kane J, Franks-Skiba K, Cimermancic P, Burlingame A, Sali A, Craik CS, Harris RS, Gross JD, Krogan NJ. PMID: 22190037; PMCID: PMC3310910.
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    198. Global landscape of HIV-human protein complexes. Nature. 2011 Dec 21; 481(7381):365-70. Jäger S, Cimermancic P, Gulbahce N, Johnson JR, McGovern KE, Clarke SC, Shales M, Mercenne G, Pache L, Li K, Hernandez H, Jang GM, Roth SL, Akiva E, Marlett J, Stephens M, D'Orso I, Fernandes J, Fahey M, Mahon C, O'Donoghue AJ, Todorovic A, Morris JH, Maltby DA, Alber T, Cagney G, Bushman FD, Young JA, Chanda SK, Sundquist WI, Kortemme T, Hernandez RD, Craik CS, Burlingame A, Sali A, Frankel AD, Krogan NJ. PMID: 22190034; PMCID: PMC3310911.
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    199. The proteasomal subunit Rpn6 is a molecular clamp holding the core and regulatory subcomplexes together. Proc Natl Acad Sci U S A. 2012 Jan 03; 109(1):149-54. Pathare GR, Nagy I, Bohn S, Unverdorben P, Hubert A, Körner R, Nickell S, Lasker K, Sali A, Tamura T, Nishioka T, Förster F, Baumeister W, Bracher A. PMID: 22187461; PMCID: PMC3252951.
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    200. Statistical potential for modeling and ranking of protein-ligand interactions. J Chem Inf Model. 2011 Dec 27; 51(12):3078-92. Fan H, Schneidman-Duhovny D, Irwin JJ, Dong G, Shoichet BK, Sali A. PMID: 22014038; PMCID: PMC3246566.
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    201. The Enzyme Function Initiative. Biochemistry. 2011 Nov 22; 50(46):9950-62. Gerlt JA, Allen KN, Almo SC, Armstrong RN, Babbitt PC, Cronan JE, Dunaway-Mariano D, Imker HJ, Jacobson MP, Minor W, Poulter CD, Raushel FM, Sali A, Shoichet BK, Sweedler JV. PMID: 21999478; PMCID: PMC3238057.
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    202. Structure meets the membrane. Structure. 2011 Oct 12; 19(10):1347. Lima C, Sali A, Kostic M. PMID: 22000504.
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    203. UCSF Chimera, MODELLER, and IMP: an integrated modeling system. J Struct Biol. 2012 Sep; 179(3):269-78. Yang Z, Lasker K, Schneidman-Duhovny D, Webb B, Huang CC, Pettersen EF, Goddard TD, Meng EC, Sali A, Ferrin TE. PMID: 21963794; PMCID: PMC3410985.
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    204. Ligand discovery from a dopamine D3 receptor homology model and crystal structure. Nat Chem Biol. 2011 Sep 18; 7(11):769-78. Carlsson J, Coleman RG, Setola V, Irwin JJ, Fan H, Schlessinger A, Sali A, Roth BL, Shoichet BK. PMID: 21926995; PMCID: PMC3197762.
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    205. Structure-based discovery of prescription drugs that interact with the norepinephrine transporter, NET. Proc Natl Acad Sci U S A. 2011 Sep 20; 108(38):15810-5. Schlessinger A, Geier E, Fan H, Irwin JJ, Shoichet BK, Giacomini KM, Sali A. PMID: 21885739; PMCID: PMC3179104.
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    206. Discovery of a cytokinin deaminase. ACS Chem Biol. 2011 Oct 21; 6(10):1036-40. Goble AM, Fan H, Sali A, Raushel FM. PMID: 21823622; PMCID: PMC3199332.
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    207. MultiFit: a web server for fitting multiple protein structures into their electron microscopy density map. Nucleic Acids Res. 2011 Jul; 39(Web Server issue):W167-70. Tjioe E, Lasker K, Webb B, Wolfson HJ, Sali A. PMID: 21715383; PMCID: PMC3125811.
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    208. Evolution: On a bender--BARs, ESCRTs, COPs, and finally getting your coat. J Cell Biol. 2011 Jun 13; 193(6):963-72. Field MC, Sali A, Rout MP. PMID: 21670211; PMCID: PMC3115789.
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    209. A conserved coatomer-related complex containing Sec13 and Seh1 dynamically associates with the vacuole in Saccharomyces cerevisiae. Mol Cell Proteomics. 2011 Jun; 10(6):M110.006478. Dokudovskaya S, Waharte F, Schlessinger A, Pieper U, Devos DP, Cristea IM, Williams R, Salamero J, Chait BT, Sali A, Field MC, Rout MP, Dargemont C. PMID: 21454883; PMCID: PMC3108837.
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    210. Structure of the C-terminal domain of Saccharomyces cerevisiae Nup133, a component of the nuclear pore complex. Proteins. 2011 May; 79(5):1672-7. Sampathkumar P, Gheyi T, Miller SA, Bain KT, Dickey M, Bonanno JB, Kim SJ, Phillips J, Pieper U, Fernandez-Martinez J, Franke JD, Martel A, Tsuruta H, Atwell S, Thompson DA, Emtage JS, Wasserman SR, Rout MP, Sali A, Sauder JM, Burley SK. PMID: 21365675; PMCID: PMC3350809.
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    211. Catalytic mechanism and three-dimensional structure of adenine deaminase. Biochemistry. 2011 Mar 22; 50(11):1917-27. Kamat SS, Bagaria A, Kumaran D, Holmes-Hampton GP, Fan H, Sali A, Sauder JM, Burley SK, Lindahl PA, Swaminathan S, Raushel FM. PMID: 21247091; PMCID: PMC3059353.
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    212. Enzymatic deamination of the epigenetic base N-6-methyladenine. J Am Chem Soc. 2011 Feb 23; 133(7):2080-3. Kamat SS, Fan H, Sauder JM, Burley SK, Shoichet BK, Sali A, Raushel FM. PMID: 21275375; PMCID: PMC3043370.
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    213. Modeling of proteins and their assemblies with the integrative modeling platform. Methods Mol Biol. 2011; 781:377-97. Webb B, Lasker K, Schneidman-Duhovny D, Tjioe E, Phillips J, Kim SJ, Velázquez-Muriel J, Russel D, Sali A. PMID: 21877292.
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    214. ModBase, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res. 2011 Jan; 39(Database issue):D465-74. Pieper U, Webb BM, Barkan DT, Schneidman-Duhovny D, Schlessinger A, Braberg H, Yang Z, Meng EC, Pettersen EF, Huang CC, Datta RS, Sampathkumar P, Madhusudhan MS, Sjölander K, Ferrin TE, Burley SK, Sali A. PMID: 21097780; PMCID: PMC3013688.
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    215. Determining macromolecular assembly structures by molecular docking and fitting into an electron density map. Proteins. 2010 Nov 15; 78(15):3205-11. Lasker K, Sali A, Wolfson HJ. PMID: 20827723; PMCID: PMC2952722.
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    216. Functional hot spots in human ATP-binding cassette transporter nucleotide binding domains. Protein Sci. 2010 Nov; 19(11):2110-21. Kelly L, Fukushima H, Karchin R, Gow JM, Chinn LW, Pieper U, Segal MR, Kroetz DL, Sali A. PMID: 20799350; PMCID: PMC3005782.
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    217. Role of organic cation transporter 3 (SLC22A3) and its missense variants in the pharmacologic action of metformin. Pharmacogenet Genomics. 2010 Nov; 20(11):687-99. Chen L, Pawlikowski B, Schlessinger A, More SS, Stryke D, Johns SJ, Portman MA, Chen E, Ferrin TE, Sali A, Giacomini KM. PMID: 20859243; PMCID: PMC2976715.
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    218. Structure of a putative BenF-like porin from Pseudomonas fluorescens Pf-5 at 2.6 A resolution. Proteins. 2010 Nov 01; 78(14):3056-62. Sampathkumar P, Lu F, Zhao X, Li Z, Gilmore J, Bain K, Rutter ME, Gheyi T, Schwinn KD, Bonanno JB, Pieper U, Fajardo JE, Fiser A, Almo SC, Swaminathan S, Chance MR, Baker D, Atwell S, Thompson DA, Emtage JS, Wasserman SR, Sali A, Sauder JM, Burley SK. PMID: 20737437; PMCID: PMC2989796.
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    219. Macromolecular docking restrained by a small angle X-ray scattering profile. J Struct Biol. 2011 Mar; 173(3):461-71. Schneidman-Duhovny D, Hammel M, Sali A. PMID: 20920583; PMCID: PMC3040266.
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    220. Structures of the autoproteolytic domain from the Saccharomyces cerevisiae nuclear pore complex component, Nup145. Proteins. 2010 Jun; 78(8):1992-8. Sampathkumar P, Ozyurt SA, Do J, Bain KT, Dickey M, Rodgers LA, Gheyi T, Sali A, Kim SJ, Phillips J, Pieper U, Fernandez-Martinez J, Franke JD, Martel A, Tsuruta H, Atwell S, Thompson DA, Emtage JS, Wasserman SR, Rout MP, Sauder JM, Burley SK. PMID: 20310066; PMCID: PMC3136511.
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    221. FoXS: a web server for rapid computation and fitting of SAXS profiles. Nucleic Acids Res. 2010 Jul; 38(Web Server issue):W540-4. Schneidman-Duhovny D, Hammel M, Sali A. PMID: 20507903; PMCID: PMC2896111.
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    222. Integrative structure modeling of macromolecular assemblies from proteomics data. Mol Cell Proteomics. 2010 Aug; 9(8):1689-702. Lasker K, Phillips JL, Russel D, Velázquez-Muriel J, Schneidman-Duhovny D, Tjioe E, Webb B, Schlessinger A, Sali A. PMID: 20507923; PMCID: PMC2938050.
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    223. Prediction of protease substrates using sequence and structure features. Bioinformatics. 2010 Jul 15; 26(14):1714-22. Barkan DT, Hostetter DR, Mahrus S, Pieper U, Wells JA, Craik CS, Sali A. PMID: 20505003; PMCID: PMC2894511.
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    224. Toward an integrated structural model of the 26S proteasome. Mol Cell Proteomics. 2010 Aug; 9(8):1666-77. Förster F, Lasker K, Nickell S, Sali A, Baumeister W. PMID: 20467039; PMCID: PMC2938054.
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    225. Function of human Rh based on structure of RhCG at 2.1 A. Proc Natl Acad Sci U S A. 2010 May 25; 107(21):9638-43. Gruswitz F, Chaudhary S, Ho JD, Schlessinger A, Pezeshki B, Ho CM, Sali A, Westhoff CM, Stroud RM. PMID: 20457942; PMCID: PMC2906887.
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    226. Comparison of human solute carriers. Protein Sci. 2010 Mar; 19(3):412-28. Schlessinger A, Matsson P, Shima JE, Pieper U, Yee SW, Kelly L, Apeltsin L, Stroud RM, Ferrin TE, Giacomini KM, Sali A. PMID: 20052679; PMCID: PMC2866268.
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    227. The overlap of small molecule and protein binding sites within families of protein structures. PLoS Comput Biol. 2010 Feb 05; 6(2):e1000668. Davis FP, Sali A. PMID: 20140189; PMCID: PMC2816688.
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    228. Comprehensive molecular structure of the eukaryotic ribosome. Structure. 2009 Dec 09; 17(12):1591-1604. Taylor DJ, Devkota B, Huang AD, Topf M, Narayanan E, Sali A, Harvey SC, Frank J. PMID: 20004163; PMCID: PMC2814252.
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    229. Molecular docking screens using comparative models of proteins. J Chem Inf Model. 2009 Nov; 49(11):2512-27. Fan H, Irwin JJ, Webb BM, Klebe G, Shoichet BK, Sali A. PMID: 19845314; PMCID: PMC2790034.
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    230. Institutional Profile: The University of California Pharmacogenomics Center: at the interface of genomics, biological mechanisms and drug therapy. Pharmacogenomics. 2009 Oct; 10(10):1569-76. Kroetz DL, Ahituv N, Burchard EG, Guo S, Sali A, Giacomini KM. PMID: 19842929; PMCID: PMC2923222.
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    231. A survey of integral alpha-helical membrane proteins. J Struct Funct Genomics. 2009 Dec; 10(4):269-80. Kelly L, Pieper U, Eswar N, Hays FA, Li M, Roe-Zurz Z, Kroetz DL, Giacomini KM, Stroud RM, Sali A. PMID: 19760129; PMCID: PMC2780624.
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    232. Global motions of the nuclear pore complex: insights from elastic network models. PLoS Comput Biol. 2009 Sep; 5(9):e1000496. Lezon TR, Sali A, Bahar I. PMID: 19730674; PMCID: PMC2725293.
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    233. An atomic model AAA-ATPase/20S core particle sub-complex of the 26S proteasome. Biochem Biophys Res Commun. 2009 Oct 16; 388(2):228-33. Förster F, Lasker K, Beck F, Nickell S, Sali A, Baumeister W. PMID: 19653995; PMCID: PMC2771176.
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    234. Alignment of multiple protein structures based on sequence and structure features. Protein Eng Des Sel. 2009 Sep; 22(9):569-74. Madhusudhan MS, Webb BM, Marti-Renom MA, Eswar N, Sali A. PMID: 19587024; PMCID: PMC2909824.
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    235. Insights into the molecular architecture of the 26S proteasome. Proc Natl Acad Sci U S A. 2009 Jul 21; 106(29):11943-7. Nickell S, Beck F, Scheres SH, Korinek A, Förster F, Lasker K, Mihalache O, Sun N, Nagy I, Sali A, Plitzko JM, Carazo JM, Mann M, Baumeister W. PMID: 19581588; PMCID: PMC2715492.
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    236. Evidence for a shared nuclear pore complex architecture that is conserved from the last common eukaryotic ancestor. Mol Cell Proteomics. 2009 Sep; 8(9):2119-30. DeGrasse JA, DuBois KN, Devos D, Siegel TN, Sali A, Field MC, Rout MP, Chait BT. PMID: 19525551; PMCID: PMC2742445.
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    237. Evolutionary constraints on structural similarity in orthologs and paralogs. Protein Sci. 2009 Jun; 18(6):1306-15. Peterson ME, Chen F, Saven JG, Roos DS, Babbitt PC, Sali A. PMID: 19472362; PMCID: PMC2774440.
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    238. Regulatory elements within the prodomain of Falcipain-2, a cysteine protease of the malaria parasite Plasmodium falciparum. PLoS One. 2009 May 27; 4(5):e5694. Pandey KC, Barkan DT, Sali A, Rosenthal PJ. PMID: 19479029; PMCID: PMC2682653.
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    239. A kernel for open source drug discovery in tropical diseases. PLoS Negl Trop Dis. 2009; 3(4):e418. Ortí L, Carbajo RJ, Pieper U, Eswar N, Maurer SM, Rai AK, Taylor G, Todd MH, Pineda-Lucena A, Sali A, Marti-Renom MA. PMID: 19381286; PMCID: PMC2667270.
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    240. ModLink+: improving fold recognition by using protein-protein interactions. Bioinformatics. 2009 Jun 15; 25(12):1506-12. Fornes O, Aragues R, Espadaler J, Marti-Renom MA, Sali A, Oliva B. PMID: 19357100; PMCID: PMC2687990.
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    241. A kernel for the Tropical Disease Initiative. Nat Biotechnol. 2009 Apr; 27(4):320-1. Ortí L, Carbajo RJ, Pieper U, Eswar N, Maurer SM, Rai AK, Taylor G, Todd MH, Pineda-Lucena A, Sali A, Marti-Renom MA. PMID: 19352362; PMCID: PMC3088649.
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    242. Inferential optimization for simultaneous fitting of multiple components into a CryoEM map of their assembly. J Mol Biol. 2009 Apr 24; 388(1):180-94. Lasker K, Topf M, Sali A, Wolfson HJ. PMID: 19233204; PMCID: PMC2680734.
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    243. The structural dynamics of macromolecular processes. Curr Opin Cell Biol. 2009 Feb; 21(1):97-108. Russel D, Lasker K, Phillips J, Schneidman-Duhovny D, Velázquez-Muriel JA, Sali A. PMID: 19223165; PMCID: PMC2774249.
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    244. Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies. J Struct Funct Genomics. 2009 Apr; 10(2):107-25. Pieper U, Chiang R, Seffernick JJ, Brown SD, Glasner ME, Kelly L, Eswar N, Sauder JM, Bonanno JB, Swaminathan S, Burley SK, Zheng X, Chance MR, Almo SC, Gerlt JA, Raushel FM, Jacobson MP, Babbitt PC, Sali A. PMID: 19219566; PMCID: PMC2693957.
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    245. Outcome of a workshop on applications of protein models in biomedical research. Structure. 2009 Feb 13; 17(2):151-9. Schwede T, Sali A, Honig B, Levitt M, Berman HM, Jones D, Brenner SE, Burley SK, Das R, Dokholyan NV, Dunbrack RL, Fidelis K, Fiser A, Godzik A, Huang YJ, Humblet C, Jacobson MP, Joachimiak A, Krystek SR, Kortemme T, Kryshtafovych A, Montelione GT, Moult J, Murray D, Sanchez R, Sosnick TR, Standley DM, Stouch T, Vajda S, Vasquez M, Westbrook JD, Wilson IA. PMID: 19217386; PMCID: PMC2739730.
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    246. 2007 annual progress report synopsis of the Center for Structures of Membrane Proteins. J Struct Funct Genomics. 2009 Apr; 10(2):193-208. Stroud RM, Choe S, Holton J, Kaback HR, Kwiatkowski W, Minor DL, Riek R, Sali A, Stahlberg H, Harries W. PMID: 19148774; PMCID: PMC2705707.
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    247. Selecting optimum eukaryotic integral membrane proteins for structure determination by rapid expression and solubilization screening. J Mol Biol. 2009 Jan 23; 385(3):820-30. Li M, Hays FA, Roe-Zurz Z, Vuong L, Kelly L, Ho CM, Robbins RM, Pieper U, O'Connell JD, Miercke LJ, Giacomini KM, Sali A, Stroud RM. PMID: 19061901; PMCID: PMC2659619.
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    248. Ratiocinative screen of eukaryotic integral membrane protein expression and solubilization for structure determination. J Struct Funct Genomics. 2009 Mar; 10(1):9-16. Hays FA, Roe-Zurz Z, Li M, Kelly L, Gruswitz F, Sali A, Stroud RM. PMID: 19031011; PMCID: PMC2756966.
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    249. MODBASE, a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res. 2009 Jan; 37(Database issue):D347-54. Pieper U, Eswar N, Webb BM, Eramian D, Kelly L, Barkan DT, Carter H, Mankoo P, Karchin R, Marti-Renom MA, Davis FP, Sali A. PMID: 18948282; PMCID: PMC2686492.
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    250. Genomic-scale prioritization of drug targets: the TDR Targets database. Nat Rev Drug Discov. 2008 11; 7(11):900-7. Agüero F, Al-Lazikani B, Aslett M, Berriman M, Buckner FS, Campbell RK, Carmona S, Carruthers IM, Chan AW, Chen F, Crowther GJ, Doyle MA, Hertz-Fowler C, Hopkins AL, McAllister G, Nwaka S, Overington JP, Pain A, Paolini GV, Pieper U, Ralph SA, Riechers A, Roos DS, Sali A, Shanmugam D, Suzuki T, Van Voorhis WC, Verlinde CL. PMID: 18927591; PMCID: PMC3184002.
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    251. How well can the accuracy of comparative protein structure models be predicted? Protein Sci. 2008 Nov; 17(11):1881-93. Eramian D, Eswar N, Shen MY, Sali A. PMID: 18832340; PMCID: PMC2578807.
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    252. Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini. Cell. 2008 Sep 05; 134(5):866-76. Mahrus S, Trinidad JC, Barkan DT, Sali A, Burlingame AL, Wells JA. PMID: 18722006; PMCID: PMC2566540.
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    253. Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies. PLoS Comput Biol. 2008 Aug 01; 4(8):e1000142. Chiang RA, Sali A, Babbitt PC. PMID: 18670595; PMCID: PMC2453236.
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    254. Integration of small-angle X-ray scattering data into structural modeling of proteins and their assemblies. J Mol Biol. 2008 Oct 17; 382(4):1089-106. Förster F, Webb B, Krukenberg KA, Tsuruta H, Agard DA, Sali A. PMID: 18694757; PMCID: PMC2745287.
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    255. Subnanometer-resolution electron cryomicroscopy-based domain models for the cytoplasmic region of skeletal muscle RyR channel. Proc Natl Acad Sci U S A. 2008 Jul 15; 105(28):9610-5. Serysheva II, Ludtke SJ, Baker ML, Cong Y, Topf M, Eramian D, Sali A, Hamilton SL, Chiu W. PMID: 18621707; PMCID: PMC2474495.
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    256. Mechanism of lid closure in the eukaryotic chaperonin TRiC/CCT. Nat Struct Mol Biol. 2008 Jul; 15(7):746-53. Booth CR, Meyer AS, Cong Y, Topf M, Sali A, Ludtke SJ, Chiu W, Frydman J. PMID: 18536725; PMCID: PMC2546500.
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    257. Prediction of enzyme function by combining sequence similarity and protein interactions. BMC Bioinformatics. 2008 May 27; 9:249. Espadaler J, Eswar N, Querol E, Avilés FX, Sali A, Marti-Renom MA, Oliva B. PMID: 18505562; PMCID: PMC2430716.
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    258. Multiple conformations of E. coli Hsp90 in solution: insights into the conformational dynamics of Hsp90. Structure. 2008 May; 16(5):755-65. Krukenberg KA, Förster F, Rice LM, Sali A, Agard DA. PMID: 18462680; PMCID: PMC2600884.
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    259. Classifying Variants of Undetermined Significance in BRCA2 with protein likelihood ratios. Cancer Inform. 2008; 6:203-16. Karchin R, Agarwal M, Sali A, Couch F, Beattie MS. PMID: 19043619; PMCID: PMC2587343.
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    260. Structure of the mammalian 80S ribosome at 8.7 A resolution. Structure. 2008 Apr; 16(4):535-48. Chandramouli P, Topf M, Ménétret JF, Eswar N, Cannone JJ, Gutell RR, Sali A, Akey CW. PMID: 18400176; PMCID: PMC2775484.
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    261. Tel2 mediates activation and localization of ATM/Tel1 kinase to a double-strand break. Genes Dev. 2008 Apr 01; 22(7):854-9. Anderson CM, Korkin D, Smith DL, Makovets S, Seidel JJ, Sali A, Blackburn EH. PMID: 18334620; PMCID: PMC2279195.
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    262. Protein structure fitting and refinement guided by cryo-EM density. Structure. 2008 Feb; 16(2):295-307. Topf M, Lasker K, Webb B, Wolfson H, Chiu W, Sali A. PMID: 18275820; PMCID: PMC2409374.
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    263. Protein production and purification. Nat Methods. 2008 Feb; 5(2):135-46. Structural Genomics Consortium, China Structural Genomics Consortium, Northeast Structural Genomics Consortium, Gräslund S, Nordlund P, Weigelt J, Hallberg BM, Bray J, Gileadi O, Knapp S, Oppermann U, Arrowsmith C, Hui R, Ming J, dhe-Paganon S, Park HW, Savchenko A, Yee A, Edwards A, Vincentelli R, Cambillau C, Kim R, Kim SH, Rao Z, Shi Y, Terwilliger TC, Kim CY, Hung LW, Waldo GS, Peleg Y, Albeck S, Unger T, Dym O, Prilusky J, Sussman JL, Stevens RC, Lesley SA, Wilson IA, Joachimiak A, Collart F, Dementieva I, Donnelly MI, Eschenfeldt WH, Kim Y, Stols L, Wu R, Zhou M, Burley SK, Emtage JS, Sauder JM, Thompson D, Bain K, Luz J, Gheyi T, Zhang F, Atwell S, Almo SC, Bonanno JB, Fiser A, Swaminathan S, Studier FW, Chance MR, Sali A, Acton TB, Xiao R, Zhao L, Ma LC, Hunt JF, Tong L, Cunningham K, Inouye M, Anderson S, Janjua H, Shastry R, Ho CK, Wang D, Wang H, Jiang M, Montelione GT, Stuart DI, Owens RJ, Daenke S, Schütz A, Heinemann U, Yokoyama S, Büssow K, Gunsalus KC. PMID: 18235434; PMCID: PMC3178102.
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    264. Protein structure modeling with MODELLER. Methods Mol Biol. 2008; 426:145-59. Eswar N, Eramian D, Webb B, Shen MY, Sali A. PMID: 18542861.
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    265. Integrating diverse data for structure determination of macromolecular assemblies. Annu Rev Biochem. 2008; 77:443-77. Alber F, Förster F, Korkin D, Topf M, Sali A. PMID: 18318657.
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    266. The molecular sociology of the cell. Nature. 2007 Dec 13; 450(7172):973-82. Robinson CV, Sali A, Baumeister W. PMID: 18075576.
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    267. Structural genomics of protein phosphatases. J Struct Funct Genomics. 2007 Sep; 8(2-3):121-40. Almo SC, Bonanno JB, Sauder JM, Emtage S, Dilorenzo TP, Malashkevich V, Wasserman SR, Swaminathan S, Eswaramoorthy S, Agarwal R, Kumaran D, Madegowda M, Ragumani S, Patskovsky Y, Alvarado J, Ramagopal UA, Faber-Barata J, Chance MR, Sali A, Fiser A, Zhang ZY, Lawrence DS, Burley SK. PMID: 18058037; PMCID: PMC4163028.
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    268. Stereochemical criteria for prediction of the effects of proline mutations on protein stability. PLoS Comput Biol. 2007 Dec; 3(12):e241. Bajaj K, Madhusudhan MS, Adkar BV, Chakrabarti P, Ramakrishnan C, Sali A, Varadarajan R. PMID: 18069886; PMCID: PMC2134964.
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    269. Determining the architectures of macromolecular assemblies. Nature. 2007 Nov 29; 450(7170):683-94. Alber F, Dokudovskaya S, Veenhoff LM, Zhang W, Kipper J, Devos D, Suprapto A, Karni-Schmidt O, Williams R, Chait BT, Rout MP, Sali A. PMID: 18046405.
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    270. The molecular architecture of the nuclear pore complex. Nature. 2007 Nov 29; 450(7170):695-701. Alber F, Dokudovskaya S, Veenhoff LM, Zhang W, Kipper J, Devos D, Suprapto A, Karni-Schmidt O, Williams R, Chait BT, Sali A, Rout MP. PMID: 18046406.
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    271. Structural genomics. Structure. 2007 Nov; 15(11):1341. Sali A, Lima CD, Kostic M. PMID: 17997955.
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    272. Comparative protein structure modeling using MODELLER. Curr Protoc Protein Sci. 2007 11; Chapter 2:Unit 2.9. Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, Shen MY, Pieper U, Sali A. PMID: 18429317.
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    273. Host pathogen protein interactions predicted by comparative modeling. Protein Sci. 2007 Dec; 16(12):2585-96. Davis FP, Barkan DT, Eswar N, McKerrow JH, Sali A. PMID: 17965183; PMCID: PMC2222825.
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    274. Crystallographic conformers of actin in a biologically active bundle of filaments. J Mol Biol. 2008 Jan 11; 375(2):331-6. Cong Y, Topf M, Sali A, Matsudaira P, Dougherty M, Chiu W, Schmid MF. PMID: 18022194; PMCID: PMC2680129.
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    275. Fold assessment for comparative protein structure modeling. Protein Sci. 2007 Nov; 16(11):2412-26. Melo F, Sali A. PMID: 17905832; PMCID: PMC2211691.
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    276. Modeling mutations in protein structures. Protein Sci. 2007 Sep; 16(9):2030-41. Feyfant E, Sali A, Fiser A. PMID: 17766392; PMCID: PMC2206969.
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    277. Characterization of protein hubs by inferring interacting motifs from protein interactions. PLoS Comput Biol. 2007 Sep; 3(9):1761-71. Aragues R, Sali A, Bonet J, Marti-Renom MA, Oliva B. PMID: 17941705; PMCID: PMC1976338.
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    278. The AnnoLite and AnnoLyze programs for comparative annotation of protein structures. BMC Bioinformatics. 2007 May 22; 8 Suppl 4:S4. Marti-Renom MA, Rossi A, Al-Shahrour F, Davis FP, Pieper U, Dopazo J, Sali A. PMID: 17570147; PMCID: PMC1892083.
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    279. DBAli tools: mining the protein structure space. Nucleic Acids Res. 2007 Jul; 35(Web Server issue):W393-7. Marti-Renom MA, Pieper U, Madhusudhan MS, Rossi A, Eswar N, Davis FP, Al-Shahrour F, Dopazo J, Sali A. PMID: 17478513; PMCID: PMC1933139.
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    280. The structure of chagasin in complex with a cysteine protease clarifies the binding mode and evolution of an inhibitor family. Structure. 2007 May; 15(5):535-43. Wang SX, Pandey KC, Scharfstein J, Whisstock J, Huang RK, Jacobelli J, Fletterick RJ, Rosenthal PJ, Abrahamson M, Brinen LS, Rossi A, Sali A, McKerrow JH. PMID: 17502099.
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    281. Lack of support for a role for RLIP76 (RALBP1) in response to treatment or predisposition to epilepsy. Epilepsia. 2007 Apr; 48(4):674-83. Soranzo N, Kelly L, Martinian L, Burley MW, Thom M, Sali A, Kroetz DL, Goldstein DB, Sisodiya SM. PMID: 17437410.
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    282. Determination of cancer risk associated with germ line BRCA1 missense variants by functional analysis. Cancer Res. 2007 Feb 15; 67(4):1494-501. Carvalho MA, Marsillac SM, Karchin R, Manoukian S, Grist S, Swaby RF, Urmenyi TP, Rondinelli E, Silva R, Gayol L, Baumbach L, Sutphen R, Pickard-Brzosowicz JL, Nathanson KL, Sali A, Goldgar D, Couch FJ, Radice P, Monteiro AN. PMID: 17308087; PMCID: PMC2936786.
      View in: PubMed   Mentions: 58     Fields:    Translation:HumansAnimals
    283. Protein interactions and disease phenotypes in the ABC transporter superfamily. Pac Symp Biocomput. 2007; 51-63. Kelly L, Karchin R, Sali A. PMID: 17990484.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    284. Functional impact of missense variants in BRCA1 predicted by supervised learning. PLoS Comput Biol. 2007 Feb 16; 3(2):e26. Karchin R, Monteiro AN, Tavtigian SV, Carvalho MA, Sali A. PMID: 17305420; PMCID: PMC1797820.
      View in: PubMed   Mentions: 32     Fields:    Translation:Cells
    285. Gene expression profiling of the human maternal-fetal interface reveals dramatic changes between midgestation and term. Endocrinology. 2007 Mar; 148(3):1059-79. Winn VD, Haimov-Kochman R, Paquet AC, Yang YJ, Madhusudhan MS, Gormley M, Feng KT, Bernlohr DA, McDonagh S, Pereira L, Sali A, Fisher SJ. PMID: 17170095.
      View in: PubMed   Mentions: 91     Fields:    Translation:Humans
    286. Statistical potential for assessment and prediction of protein structures. Protein Sci. 2006 Nov; 15(11):2507-24. Shen MY, Sali A. PMID: 17075131; PMCID: PMC2242414.
      View in: PubMed   Mentions: 1093     Fields:    Translation:Cells
    287. Structural modeling of protein interactions by analogy: application to PSD-95. PLoS Comput Biol. 2006 Nov 10; 2(11):e153. Korkin D, Davis FP, Alber F, Luong T, Shen MY, Lucic V, Kennedy MB, Sali A. PMID: 17096593; PMCID: PMC1635541.
      View in: PubMed   Mentions: 18     Fields:    Translation:Cells
    288. Comparative protein structure modeling using Modeller. Curr Protoc Bioinformatics. 2006 Oct; Chapter 5:Unit-5.6. Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, Shen MY, Pieper U, Sali A. PMID: 18428767; PMCID: PMC4186674.
      View in: PubMed   Mentions: 1227     Fields:    Translation:Cells
    289. Localization of binding sites in protein structures by optimization of a composite scoring function. Protein Sci. 2006 Oct; 15(10):2366-80. Rossi A, Marti-Renom MA, Sali A. PMID: 16963645; PMCID: PMC2242385.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    290. Minimalist representations and the importance of nearest neighbor effects in protein folding simulations. J Mol Biol. 2006 Nov 03; 363(4):835-57. Colubri A, Jha AK, Shen MY, Sali A, Berry RS, Sosnick TR, Freed KF. PMID: 16982067.
      View in: PubMed   Mentions: 24     Fields:    Translation:Cells
    291. Outcome of a workshop on archiving structural models of biological macromolecules. Structure. 2006 Aug; 14(8):1211-7. Berman HM, Burley SK, Chiu W, Sali A, Adzhubei A, Bourne PE, Bryant SH, Dunbrack RL, Fidelis K, Frank J, Godzik A, Henrick K, Joachimiak A, Heymann B, Jones D, Markley JL, Moult J, Montelione GT, Orengo C, Rossmann MG, Rost B, Saibil H, Schwede T, Standley DM, Westbrook JD. PMID: 16955948.
      View in: PubMed   Mentions: 27     Fields:    
    292. A composite score for predicting errors in protein structure models. Protein Sci. 2006 Jul; 15(7):1653-66. Eramian D, Shen MY, Devos D, Melo F, Sali A, Marti-Renom MA. PMID: 16751606; PMCID: PMC2242555.
      View in: PubMed   Mentions: 83     Fields:    
    293. Protein complex compositions predicted by structural similarity. Nucleic Acids Res. 2006; 34(10):2943-52. Davis FP, Braberg H, Shen MY, Pieper U, Sali A, Madhusudhan MS. PMID: 16738133; PMCID: PMC1474056.
      View in: PubMed   Mentions: 26     Fields:    Translation:Cells
    294. Protease accessibility laddering: a proteomic tool for probing protein structure. Structure. 2006 Apr; 14(4):653-60. Dokudovskaya S, Williams R, Devos D, Sali A, Chait BT, Rout MP. PMID: 16615907.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansAnimalsCells
    295. PharmGKB submission update: IV. PMT submissions of genetic variations in ATP-Binding cassette transporters to the PharmGKB network. Pharmacol Rev. 2006 Mar; 58(1):1-2. Nguyen TD, Gow JM, Chinn LW, Kelly L, Jeong H, Huang CC, Stryke D, Kawamoto M, Johns SJ, Carlson E, Taylor T, Ferrin TE, Sali A, Giacomini KM, Kroetz DL. PMID: 16507877.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    296. Simple fold composition and modular architecture of the nuclear pore complex. Proc Natl Acad Sci U S A. 2006 Feb 14; 103(7):2172-7. Devos D, Dokudovskaya S, Williams R, Alber F, Eswar N, Chait BT, Rout MP, Sali A. PMID: 16461911; PMCID: PMC1413685.
      View in: PubMed   Mentions: 142     Fields:    Translation:AnimalsCells
    297. Refinement of protein structures by iterative comparative modeling and CryoEM density fitting. J Mol Biol. 2006 Apr 14; 357(5):1655-68. Topf M, Baker ML, Marti-Renom MA, Chiu W, Sali A. PMID: 16490207.
      View in: PubMed   Mentions: 56     Fields:    Translation:Cells
    298. Variable gap penalty for protein sequence-structure alignment. Protein Eng Des Sel. 2006 Mar; 19(3):129-33. Madhusudhan MS, Marti-Renom MA, Sanchez R, Sali A. PMID: 16423846.
      View in: PubMed   Mentions: 30     Fields:    Translation:Cells
    299. MODBASE: a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res. 2006 Jan 01; 34(Database issue):D291-5. Pieper U, Eswar N, Davis FP, Braberg H, Madhusudhan MS, Rossi A, Marti-Renom M, Karchin R, Webb BM, Eramian D, Shen MY, Kelly L, Melo F, Sali A. PMID: 16381869; PMCID: PMC1347422.
      View in: PubMed   Mentions: 108     Fields:    Translation:HumansCells
    300. Combining electron microscopy and comparative protein structure modeling. Curr Opin Struct Biol. 2005 Oct; 15(5):578-85. Topf M, Sali A. PMID: 16118050.
      View in: PubMed   Mentions: 29     Fields:    Translation:Cells
    301. The C-type lectin fold as an evolutionary solution for massive sequence variation. Nat Struct Mol Biol. 2005 Oct; 12(10):886-92. McMahon SA, Miller JL, Lawton JA, Kerkow DE, Hodes A, Marti-Renom MA, Doulatov S, Narayanan E, Sali A, Miller JF, Ghosh P. PMID: 16170324.
      View in: PubMed   Mentions: 53     Fields:    Translation:Cells
    302. Localization of protein-binding sites within families of proteins. Protein Sci. 2005 Sep; 14(9):2350-60. Korkin D, Davis FP, Sali A. PMID: 16081657; PMCID: PMC2253467.
      View in: PubMed   Mentions: 21     Fields:    Translation:Cells
    303. Multiple cathepsin B isoforms in schistosomula of Trichobilharzia regenti: identification, characterisation and putative role in migration and nutrition. Int J Parasitol. 2005 Jul; 35(8):895-910. Dvorák J, Delcroix M, Rossi A, Vopálenský V, Pospísek M, Sedinová M, Mikes L, Sajid M, Sali A, McKerrow JH, Horák P, Caffrey CR. PMID: 15950230.
      View in: PubMed   Mentions: 17     Fields:    Translation:AnimalsCells
    304. Detecting remotely related proteins by their interactions and sequence similarity. Proc Natl Acad Sci U S A. 2005 May 17; 102(20):7151-6. Espadaler J, Aragüés R, Eswar N, Marti-Renom MA, Querol E, Avilés FX, Sali A, Oliva B. PMID: 15883372; PMCID: PMC1129109.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
    305. LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources. Bioinformatics. 2005 Jun 15; 21(12):2814-20. Karchin R, Diekhans M, Kelly L, Thomas DJ, Pieper U, Eswar N, Haussler D, Sali A. PMID: 15827081.
      View in: PubMed   Mentions: 103     Fields:    
    306. Structural characterization of assemblies from overall shape and subcomplex compositions. Structure. 2005 Mar; 13(3):435-45. Alber F, Kim MF, Sali A. PMID: 15766545.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    307. Urokinase-type plasminogen activator is a preferred substrate of the human epithelium serine protease tryptase epsilon/PRSS22. Blood. 2005 May 15; 105(10):3893-901. Yasuda S, Morokawa N, Wong GW, Rossi A, Madhusudhan MS, Sali A, Askew YS, Adachi R, Silverman GA, Krilis SA, Stevens RL. PMID: 15701722; PMCID: PMC1895090.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansAnimalsCells
    308. Structural characterization of components of protein assemblies by comparative modeling and electron cryo-microscopy. J Struct Biol. 2005 Feb; 149(2):191-203. Topf M, Baker ML, John B, Chiu W, Sali A. PMID: 15681235.
      View in: PubMed   Mentions: 46     Fields:    Translation:Cells
    309. PIBASE: a comprehensive database of structurally defined protein interfaces. Bioinformatics. 2005 May 01; 21(9):1901-7. Davis FP, Sali A. PMID: 15657096.
      View in: PubMed   Mentions: 76     Fields:    Translation:Cells
    310. New York-Structural GenomiX Research Consortium (NYSGXRC): a large scale center for the protein structure initiative. J Struct Funct Genomics. 2005; 6(2-3):225-32. Bonanno JB, Almo SC, Bresnick A, Chance MR, Fiser A, Swaminathan S, Jiang J, Studier FW, Shapiro L, Lima CD, Gaasterland TM, Sali A, Bain K, Feil I, Gao X, Lorimer D, Ramos A, Sauder JM, Wasserman SR, Emtage S, D'Amico KL, Burley SK. PMID: 16211523.
      View in: PubMed   Mentions: 19     Fields:    
    311. Improving functional annotation of non-synonomous SNPs with information theory. Pac Symp Biocomput. 2005; 397-408. Karchin R, Kelly L, Sali A. PMID: 15759645.
      View in: PubMed   Mentions: 17     Fields:    Translation:Cells
    312. Finding cures for tropical diseases: is open source an answer? PLoS Med. 2004 Dec; 1(3):e56. Maurer SM, Rai A, Sali A. PMID: 15630466; PMCID: PMC539047.
      View in: PubMed   Mentions: 21     Fields:    Translation:Humans
    313. Components of coated vesicles and nuclear pore complexes share a common molecular architecture. PLoS Biol. 2004 Dec; 2(12):e380. Devos D, Dokudovskaya S, Alber F, Williams R, Chait BT, Sali A, Rout MP. PMID: 15523559; PMCID: PMC524472.
      View in: PubMed   Mentions: 191     Fields:    Translation:AnimalsCells
    314. High-throughput computational and experimental techniques in structural genomics. Genome Res. 2004 Oct; 14(10B):2145-54. Chance MR, Fiser A, Sali A, Pieper U, Eswar N, Xu G, Fajardo JE, Radhakannan T, Marinkovic N. PMID: 15489337; PMCID: PMC528931.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansAnimalsCells
    315. A structural perspective on protein-protein interactions. Curr Opin Struct Biol. 2004 Jun; 14(3):313-24. Russell RB, Alber F, Aloy P, Davis FP, Korkin D, Pichaud M, Topf M, Sali A. PMID: 15193311.
      View in: PubMed   Mentions: 79     Fields:    Translation:HumansAnimalsCells
    316. Structure-based assessment of missense mutations in human BRCA1: implications for breast and ovarian cancer predisposition. Cancer Res. 2004 Jun 01; 64(11):3790-7. Mirkovic N, Marti-Renom MA, Weber BL, Sali A, Monteiro AN. PMID: 15172985.
      View in: PubMed   Mentions: 47     Fields:    Translation:HumansCells
    317. Comprehensive search for cysteine cathepsins in the human genome. Biol Chem. 2004 May; 385(5):363-72. Rossi A, Deveraux Q, Turk B, Sali A. PMID: 15195995.
      View in: PubMed   Mentions: 50     Fields:    Translation:Humans
    318. Alignment of protein sequences by their profiles. Protein Sci. 2004 Apr; 13(4):1071-87. Marti-Renom MA, Madhusudhan MS, Sali A. PMID: 15044736; PMCID: PMC2280052.
      View in: PubMed   Mentions: 81     Fields:    Translation:Cells
    319. MODBASE, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res. 2004 Jan 01; 32(Database issue):D217-22. Pieper U, Eswar N, Braberg H, Madhusudhan MS, Davis FP, Stuart AC, Mirkovic N, Rossi A, Marti-Renom MA, Fiser A, Webb B, Greenblatt D, Huang CC, Ferrin TE, Sali A. PMID: 14681398; PMCID: PMC308829.
      View in: PubMed   Mentions: 87     Fields:    Translation:HumansAnimalsCells
    320. Detection of homologous proteins by an intermediate sequence search. Protein Sci. 2004 Jan; 13(1):54-62. John B, Sali A. PMID: 14691221; PMCID: PMC2286512.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    321. ModLoop: automated modeling of loops in protein structures. Bioinformatics. 2003 Dec 12; 19(18):2500-1. Fiser A, Sali A. PMID: 14668246.
      View in: PubMed   Mentions: 311     Fields:    Translation:Cells
    322. NIH workshop on structural proteomics of biological complexes. Structure. 2003 Sep; 11(9):1043-7. Sali A. PMID: 12962622.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    323. Comparative protein structure modeling by iterative alignment, model building and model assessment. Nucleic Acids Res. 2003 Jul 15; 31(14):3982-92. John B, Sali A. PMID: 12853614; PMCID: PMC165975.
      View in: PubMed   Mentions: 122     Fields:    Translation:Cells
    324. EVA: Evaluation of protein structure prediction servers. Nucleic Acids Res. 2003 Jul 01; 31(13):3311-5. Koh IY, Eyrich VA, Marti-Renom MA, Przybylski D, Madhusudhan MS, Eswar N, Graña O, Pazos F, Valencia A, Sali A, Rost B. PMID: 12824315; PMCID: PMC169025.
      View in: PubMed   Mentions: 43     Fields:    Translation:Cells
    325. Tools for comparative protein structure modeling and analysis. Nucleic Acids Res. 2003 Jul 01; 31(13):3375-80. Eswar N, John B, Mirkovic N, Fiser A, Ilyin VA, Pieper U, Stuart AC, Marti-Renom MA, Madhusudhan MS, Yerkovich B, Sali A. PMID: 12824331; PMCID: PMC168950.
      View in: PubMed   Mentions: 202     Fields:    Translation:Cells
    326. Study of the structural dynamics of the E coli 70S ribosome using real-space refinement. Cell. 2003 Jun 13; 113(6):789-801. Gao H, Sengupta J, Valle M, Korostelev A, Eswar N, Stagg SM, Van Roey P, Agrawal RK, Harvey SC, Sali A, Chapman MS, Frank J. PMID: 12809609.
      View in: PubMed   Mentions: 109     Fields:    Translation:Cells
    327. The zebrafish forkhead transcription factor Foxi1 specifies epibranchial placode-derived sensory neurons. Development. 2003 Jun; 130(12):2669-79. Lee SA, Shen EL, Fiser A, Sali A, Guo S. PMID: 12736211.
      View in: PubMed   Mentions: 15     Fields:    Translation:AnimalsCells
    328. From words to literature in structural proteomics. Nature. 2003 Mar 13; 422(6928):216-25. Sali A, Glaeser R, Earnest T, Baumeister W. PMID: 12634795.
      View in: PubMed   Mentions: 111     Fields:    Translation:HumansAnimalsCells
    329. Modeller: generation and refinement of homology-based protein structure models. Methods Enzymol. 2003; 374:461-91. Fiser A, Sali A. PMID: 14696385.
      View in: PubMed   Mentions: 720     Fields:    Translation:AnimalsCells
    330. ModView, visualization of multiple protein sequences and structures. Bioinformatics. 2003 Jan; 19(1):165-6. Ilyin VA, Pieper U, Stuart AC, Marti-Renom MA, McMahan L, Sali A. PMID: 12499313.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    331. Use of single point mutations in domain I of beta 2-glycoprotein I to determine fine antigenic specificity of antiphospholipid autoantibodies. J Immunol. 2002 Dec 15; 169(12):7097-103. Iverson GM, Reddel S, Victoria EJ, Cockerill KA, Wang YX, Marti-Renom MA, Sali A, Marquis DM, Krilis SA, Linnik MD. PMID: 12471146.
      View in: PubMed   Mentions: 30     Fields:    Translation:HumansCells
    332. Evolution and physics in comparative protein structure modeling. Acc Chem Res. 2002 Jun; 35(6):413-21. Fiser A, Feig M, Brooks CL, Sali A. PMID: 12069626.
      View in: PubMed   Mentions: 29     Fields:    Translation:Cells
    333. Probing the specificity of a trypanosomal aromatic alpha-hydroxy acid dehydrogenase by site-directed mutagenesis. Biochem Biophys Res Commun. 2002 Apr 26; 293(1):633-9. Vernal J, Fiser A, Sali A, Müller M, Cazzulo JJ, Nowicki C. PMID: 12054650.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCells
    334. RasGRP4, a new mast cell-restricted Ras guanine nucleotide-releasing protein with calcium- and diacylglycerol-binding motifs. Identification of defective variants of this signaling protein in asthma, mastocytosis, and mast cell leukemia patients and demonstration of the importance of RasGRP4 in mast cell development and function. J Biol Chem. 2002 Jul 12; 277(28):25756-74. Yang Y, Li L, Wong GW, Krilis SA, Madhusudhan MS, Sali A, Stevens RL. PMID: 11956218.
      View in: PubMed   Mentions: 44     Fields:    Translation:HumansAnimalsCells
    335. Structural genomics: a pipeline for providing structures for the biologist. Protein Sci. 2002 Apr; 11(4):723-38. Chance MR, Bresnick AR, Burley SK, Jiang JS, Lima CD, Sali A, Almo SC, Bonanno JB, Buglino JA, Boulton S, Chen H, Eswar N, He G, Huang R, Ilyin V, McMahan L, Pieper U, Ray S, Vidal M, Wang LK. PMID: 11910018; PMCID: PMC2373525.
      View in: PubMed   Mentions: 56     Fields:    Translation:HumansAnimalsCells
    336. Reliability of assessment of protein structure prediction methods. Structure. 2002 Mar; 10(3):435-40. Marti-Renom MA, Madhusudhan MS, Fiser A, Rost B, Sali A. PMID: 12005441.
      View in: PubMed   Mentions: 36     Fields:    Translation:HumansCells
    337. Statistical potentials for fold assessment. Protein Sci. 2002 Feb; 11(2):430-48. Melo F, Sánchez R, Sali A. PMID: 11790853; PMCID: PMC2373452.
      View in: PubMed   Mentions: 155     Fields:    Translation:Cells
    338. LigBase: a database of families of aligned ligand binding sites in known protein sequences and structures. Bioinformatics. 2002 Jan; 18(1):200-1. Stuart AC, Ilyin VA, Sali A. PMID: 11836232.
      View in: PubMed   Mentions: 28     Fields:    Translation:Cells
    339. MODBASE, a database of annotated comparative protein structure models. Nucleic Acids Res. 2002 Jan 01; 30(1):255-9. Pieper U, Eswar N, Stuart AC, Ilyin VA, Sali A. PMID: 11752309; PMCID: PMC99112.
      View in: PubMed   Mentions: 36     Fields:    Translation:HumansAnimalsCells
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