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2020 – today
- 2025
[j123]Sophia M. N. Hönig
, Torben Gutermuth, Christiane Ehrt, Christian Lemmen, Matthias Rarey:
Combining crystallographic and binding affinity data towards a novel dataset of small molecule overlays. J. Comput. Aided Mol. Des. 39(1): 2 (2025)- [c6]Martin Poppinga, Annett Ungethüm, Matthias Rarey:
Caching Partition Identifiers for Fast Geometric Pattern Matching. BTW 2025: 499-521 - 2024
- [j122]Sophia M. N. Hönig, Florian Flachsenberg, Christiane Ehrt, Alexander Neumann, Robert Schmidt, Christian Lemmen, Matthias Rarey:
SpaceGrow: efficient shape-based virtual screening of billion-sized combinatorial fragment spaces. J. Comput. Aided Mol. Des. 38(1): 13 (2024) - [j121]Konrad Diedrich, Christiane Ehrt, Joel Graef, Martin Poppinga, Norbert Ritter, Matthias Rarey:
User-centric design of a 3D search interface for protein-ligand complexes. J. Comput. Aided Mol. Des. 38(1): 23 (2024) - [j120]Florian Flachsenberg, Christiane Ehrt, Torben Gutermuth, Matthias Rarey:
Redocking the PDB. J. Chem. Inf. Model. 64(1): 219-237 (2024) - [j119]Justin Lübbers, Uta F. Lessel, Matthias Rarey:
Enhanced Calculation of Property Distributions in Chemical Fragment Spaces. J. Chem. Inf. Model. 64(6): 2008-2020 (2024) - [j118]Joel Graef, Christiane Ehrt, Thorben Reim, Matthias Rarey:
Database-Driven Identification of Structurally Similar Protein-Protein Interfaces. J. Chem. Inf. Model. 64(8): 3332-3349 (2024) - [d4]Joel Graef, Christiane Ehrt, Thorben Reim, Matthias Rarey:
Optimization and Evaluation Datasets for PiMine. Version 2. UHH-FDR, 2024 [all versions]
- [d3]Joel Graef, Christiane Ehrt, Thorben Reim, Matthias Rarey:
Optimization and Evaluation Datasets for PiMine. Version 3. UHH-FDR, 2024 [all versions] - 2023
- [j117]Jochen Sieg, Matthias Rarey:
Searching similar local 3D micro-environments in protein structure databases with MicroMiner. Briefings Bioinform. 24(6) (2023) - [j116]Christian Meyenburg, Uschi Dolfus, Hans Briem, Matthias Rarey:
Galileo: Three-dimensional searching in large combinatorial fragment spaces on the example of pharmacophores. J. Comput. Aided Mol. Des. 37(1): 1-16 (2023) - [j115]Konrad Diedrich, Bennet Krause, Ole Berg, Matthias Rarey:
PoseEdit: enhanced ligand binding mode communication by interactive 2D diagrams. J. Comput. Aided Mol. Des. 37(10): 491-503 (2023) - [j114]Karla Gonzalez-Ponce, Carolina Horta Andrade, Fiona M. I. Hunter, Johannes Kirchmair, Karina Martínez-Mayorga, José L. Medina-Franco, Matthias Rarey, Alexander Tropsha, Alexandre Varnek, Barbara Zdrazil:
School of cheminformatics in Latin America. J. Cheminformatics 15(1): 82 (2023) - [j113]Torben Gutermuth, Jochen Sieg, Tim Stohn, Matthias Rarey:
Modeling with Alternate Locations in X-ray Protein Structures. J. Chem. Inf. Model. 63(8): 2573-2585 (2023) - [j112]Joel Graef, Christiane Ehrt, Matthias Rarey:
Binding Site Detection Remastered: Enabling Fast, Robust, and Reliable Binding Site Detection and Descriptor Calculation with DoGSite3. J. Chem. Inf. Model. 63(10): 3128-3137 (2023) - [j111]Uschi Dolfus, Hans Briem, Torben Gutermuth, Matthias Rarey:
Full Modification Control over Retrosynthetic Routes for Guided Optimization of Lead Structures. J. Chem. Inf. Model. 63(21): 6587-6597 (2023) - [c5]Martin Poppinga, Joel Graef, Konrad Diedrich, Matthias Rarey, Norbert Ritter:
Database and Workflow Optimizations for Spatial-Geometric Queries in GeoMine. LWDA 2023: 86-97 - [d2]Joel Graef, Christiane Ehrt, Thorben Reim, Matthias Rarey:
Optimization and Evaluation Datasets for PiMine. Version 1. UHH-FDR, 2023 [all versions] - [d1]Jochen Sieg, Matthias Rarey:
Single mutation protein structure pairs extracted from the PDB with MicroMiner. UHH-FDR, 2023 - 2022
- [j110]Patrick Penner, Virginie Y. Martiny, Louis Bellmann, Florian Flachsenberg, Marcus Gastreich, Isabelle Theret, Christophe Meyer, Matthias Rarey:
FastGrow: on-the-fly growing and its application to DYRK1A. J. Comput. Aided Mol. Des. 36(9): 639-651 (2022) - [j109]Tobias Harren, Hans Matter, Gerhard Hessler, Matthias Rarey, Christoph Grebner:
Interpretation of Structure-Activity Relationships in Real-World Drug Design Data Sets Using Explainable Artificial Intelligence. J. Chem. Inf. Model. 62(3): 447-462 (2022) - [j108]Louis Bellmann, Patrick Penner, Marcus Gastreich, Matthias Rarey:
Comparison of Combinatorial Fragment Spaces and Its Application to Ultralarge Make-on-Demand Compound Catalogs. J. Chem. Inf. Model. 62(3): 553-566 (2022) - [j107]Patrick Penner, Wolfgang Guba, Robert Schmidt, Agnes Meyder, Martin Stahl, Matthias Rarey:
The Torsion Library: Semiautomated Improvement of Torsion Rules with SMARTScompare. J. Chem. Inf. Model. 62(7): 1644-1653 (2022) - [j106]Matthias Rarey, Marc C. Nicklaus, Wendy A. Warr:
Special Issue on Reaction Informatics and Chemical Space. J. Chem. Inf. Model. 62(9): 2009-2010 (2022) - [j105]Wendy A. Warr, Marc C. Nicklaus, Christos A. Nicolaou, Matthias Rarey:
Exploration of Ultralarge Compound Collections for Drug Discovery. J. Chem. Inf. Model. 62(9): 2021-2034 (2022) - [j104]Robert Schmidt, Raphael Klein, Matthias Rarey:
Maximum Common Substructure Searching in Combinatorial Make-on-Demand Compound Spaces. J. Chem. Inf. Model. 62(9): 2133-2150 (2022) - [j103]Louis Bellmann, Raphael Klein, Matthias Rarey:
Calculating and Optimizing Physicochemical Property Distributions of Large Combinatorial Fragment Spaces. J. Chem. Inf. Model. 62(11): 2800-2810 (2022) - [j102]Uschi Dolfus, Hans Briem, Matthias Rarey:
Synthesis-Aware Generation of Structural Analogues. J. Chem. Inf. Model. 62(15): 3565-3576 (2022) - [j101]Uschi Dolfus, Hans Briem, Matthias Rarey:
Visualizing Generic Reaction Patterns. J. Chem. Inf. Model. 62(19): 4680-4689 (2022) - [j100]Katrin Schöning-Stierand, Konrad Diedrich, Christiane Ehrt, Florian Flachsenberg, Joel Graef, Jochen Sieg, Patrick Penner, Martin Poppinga, Annett Ungethüm, Matthias Rarey:
ProteinsPlus: a comprehensive collection of web-based molecular modeling tools. Nucleic Acids Res. 50(W1): 611-615 (2022) - 2021
- [j99]Konrad Diedrich, Joel Graef, Katrin Schöning-Stierand, Matthias Rarey:
GeoMine: interactive pattern mining of protein-ligand interfaces in the Protein Data Bank. Bioinform. 37(3): 424-425 (2021) - [j98]Florian Flachsenberg, Matthias Rarey:
LSLOpt: An open-source implementation of the step-length controlled LSL-BFGS algorithm. J. Comput. Chem. 42(15): 1095-1100 (2021) - [j97]Robert Schmidt, Florian Krull, Anna Lina Heinzke, Matthias Rarey:
Disconnected Maximum Common Substructures under Constraints. J. Chem. Inf. Model. 61(1): 167-178 (2021) - [j96]Louis Bellmann, Patrick Penner, Matthias Rarey:
Topological Similarity Search in Large Combinatorial Fragment Spaces. J. Chem. Inf. Model. 61(1): 238-251 (2021) - [j95]Matthias Rarey, Marc C. Nicklaus, Wendy A. Warr:
Call for Papers for the Special Issue: From Reaction Informatics to Chemical Space. J. Chem. Inf. Model. 61(4): 1531-1532 (2021) - 2020
- [j94]Kenneth M. Merz Jr., Rommie E. Amaro, Zoe Cournia, Matthias Rarey, Thereza A. Soares, Alexander Tropsha, Habibah A. Wahab, Renxiao Wang:
Editorial: Method and Data Sharing and Reproducibility of Scientific Results. J. Chem. Inf. Model. 60(12): 5868-5869 (2020) - [j93]Patrick Penner, Virginie Y. Martiny, Arnaud Gohier, Marcus Gastreich, Pierre Ducrot, David Brown, Matthias Rarey:
Shape-Based Descriptors for Efficient Structure-Based Fragment Growing. J. Chem. Inf. Model. 60(12): 6269-6281 (2020) - [j92]Florian Flachsenberg, Agnes Meyder, Kai Sommer, Patrick Penner, Matthias Rarey:
A Consistent Scheme for Gradient-Based Optimization of Protein-Ligand Poses. J. Chem. Inf. Model. 60(12): 6502-6522 (2020) - [j91]Katrin Schöning-Stierand, Konrad Diedrich, Rainer Fährrolfes, Florian Flachsenberg, Agnes Meyder, Eva Nittinger, Ruben Steinegger, Matthias Rarey:
ProteinsPlus: interactive analysis of protein-ligand binding interfaces. Nucleic Acids Res. 48(Webserver-Issue): W48-W53 (2020) - no results
2010 – 2019
- 2019
- [j90]Agnes Meyder, Stefanie Kampen, Jochen Sieg, Rainer Fährrolfes, Nils-Ole Friedrich, Florian Flachsenberg, Matthias Rarey:
StructureProfiler: an all-in-one tool for 3D protein structure profiling. Bioinform. 35(5): 874-876 (2019) - [j89]Nils-Ole Friedrich, Florian Flachsenberg, Agnes Meyder, Kai Sommer, Johannes Kirchmair, Matthias Rarey:
Conformator: A Novel Method for the Generation of Conformer Ensembles. J. Chem. Inf. Model. 59(2): 731-742 (2019) - [j88]Günter Klambauer, Sepp Hochreiter, Matthias Rarey:
Machine Learning in Drug Discovery. J. Chem. Inf. Model. 59(3): 945-946 (2019) - [j87]Jochen Sieg, Florian Flachsenberg, Matthias Rarey:
In Need of Bias Control: Evaluating Chemical Data for Machine Learning in Structure-Based Virtual Screening. J. Chem. Inf. Model. 59(3): 947-961 (2019) - [j86]Robert Schmidt, Emanuel S. R. Ehmki, Farina Ohm, Hans-Christian Ehrlich, Andriy Mashychev, Matthias Rarey:
Comparing Molecular Patterns Using the Example of SMARTS: Theory and Algorithms. J. Chem. Inf. Model. 59(6): 2560-2571 (2019) - [j85]Emanuel S. R. Ehmki, Robert Schmidt, Farina Ohm, Matthias Rarey:
Comparing Molecular Patterns Using the Example of SMARTS: Applications and Filter Collection Analysis. J. Chem. Inf. Model. 59(6): 2572-2586 (2019) - [j84]Louis Bellmann, Patrick Penner, Matthias Rarey:
Connected Subgraph Fingerprints: Representing Molecules Using Exhaustive Subgraph Enumeration. J. Chem. Inf. Model. 59(11): 4625-4635 (2019) - 2018
- [j83]Eva Nittinger, Florian Flachsenberg, Stefan Bietz, Gudrun Lange, Robert Klein, Matthias Rarey:
Placement of Water Molecules in Protein Structures: From Large-Scale Evaluations to Single-Case Examples. J. Chem. Inf. Model. 58(8): 1625-1637 (2018) - [j82]Sepp Hochreiter, Günter Klambauer, Matthias Rarey:
Machine Learning in Drug Discovery. J. Chem. Inf. Model. 58(9): 1723-1724 (2018) - 2017
- [j81]Mathias M. von Behren, Matthias Rarey:
Ligand-based virtual screening under partial shape constraints. J. Comput. Aided Mol. Des. 31(4): 335-347 (2017) - [j80]Florian Flachsenberg, Niek Andresen, Matthias Rarey:
RingDecomposerLib: An Open-Source Implementation of Unique Ring Families and Other Cycle Bases. J. Chem. Inf. Model. 57(2): 122-126 (2017) - [j79]Therese Inhester, Stefan Bietz, Matthias Hilbig, Robert Schmidt, Matthias Rarey:
Index-Based Searching of Interaction Patterns in Large Collections of Protein-Ligand Interfaces. J. Chem. Inf. Model. 57(2): 148-158 (2017) - [j78]Nils-Ole Friedrich, Agnes Meyder, Christina de Bruyn Kops, Kai Sommer, Florian Flachsenberg, Matthias Rarey, Johannes Kirchmair:
High-Quality Dataset of Protein-Bound Ligand Conformations and Its Application to Benchmarking Conformer Ensemble Generators. J. Chem. Inf. Model. 57(3): 529-539 (2017) - [j77]Therese Inhester, Eva Nittinger, Kai Sommer, Pascal Schmidt, Stefan Bietz, Matthias Rarey:
NAOMInova: Interactive Geometric Analysis of Noncovalent Interactions in Macromolecular Structures. J. Chem. Inf. Model. 57(9): 2132-2142 (2017) - [j76]Agnes Meyder, Eva Nittinger, Gudrun Lange, Robert Klein, Matthias Rarey:
Estimating Electron Density Support for Individual Atoms and Molecular Fragments in X-ray Structures. J. Chem. Inf. Model. 57(10): 2437-2447 (2017) - [j75]Nils-Ole Friedrich, Christina de Bruyn Kops, Florian Flachsenberg, Kai Sommer, Matthias Rarey, Johannes Kirchmair:
Benchmarking Commercial Conformer Ensemble Generators. J. Chem. Inf. Model. 57(11): 2719-2728 (2017) - [j74]Rainer Fährrolfes, Stefan Bietz, Florian Flachsenberg, Agnes Meyder, Eva Nittinger, Thomas Otto, Andrea Volkamer, Matthias Rarey:
ProteinsPlus: a web portal for structure analysis of macromolecules. Nucleic Acids Res. 45(Webserver-Issue): W337-W343 (2017) - 2016
- [j73]Mathias M. von Behren, Stefan Bietz, Eva Nittinger, Matthias Rarey:
mRAISE: an alternative algorithmic approach to ligand-based virtual screening. J. Comput. Aided Mol. Des. 30(8): 583-594 (2016) - [j72]Wolfgang Guba, Agnes Meyder, Matthias Rarey, Jérôme Hert:
Torsion Library Reloaded: A New Version of Expert-Derived SMARTS Rules for Assessing Conformations of Small Molecules. J. Chem. Inf. Model. 56(1): 1-5 (2016) - [j71]Tobias Lang, Florian Flachsenberg, Ulrike von Luxburg, Matthias Rarey:
Feasibility of Active Machine Learning for Multiclass Compound Classification. J. Chem. Inf. Model. 56(1): 12-20 (2016) - [j70]Stefan Bietz, Matthias Rarey:
SIENA: Efficient Compilation of Selective Protein Binding Site Ensembles. J. Chem. Inf. Model. 56(1): 248-259 (2016) - [j69]Kai Sommer, Nils-Ole Friedrich, Stefan Bietz, Matthias Hilbig, Therese Inhester, Matthias Rarey:
UNICON: A Powerful and Easy-to-Use Compound Library Converter. J. Chem. Inf. Model. 56(6): 1105-1111 (2016) - [j68]Florian Lauck, Matthias Rarey:
FSees: Customized Enumeration of Chemical Subspaces with Limited Main Memory Consumption. J. Chem. Inf. Model. 56(9): 1641-1653 (2016) - 2015
- [j67]Kenneth M. Merz Jr., Matthias Rarey, Alexander Tropsha, Habibah A. Wahab:
Letter from the Editors. J. Chem. Inf. Model. 55(4): 719-720 (2015) - [j66]Eva Nittinger, Nadine Schneider, Gudrun Lange, Matthias Rarey:
Evidence of Water Molecules - A Statistical Evaluation of Water Molecules Based on Electron Density. J. Chem. Inf. Model. 55(4): 771-783 (2015) - [j65]Markus Wagener, Frank Oellien, Uli Fechner, Matthias Rarey:
10th ICCS/GCC Conference: 40 Years of Cheminformatics. J. Chem. Inf. Model. 55(6): 1087 (2015) - [j64]Stefan Bietz, Karen T. Schomburg, Matthias Hilbig, Matthias Rarey:
Discriminative Chemical Patterns: Automatic and Interactive Design. J. Chem. Inf. Model. 55(8): 1535-1546 (2015) - [j63]Stefan Bietz, Matthias Rarey:
ASCONA: Rapid Detection and Alignment of Protein Binding Site Conformations. J. Chem. Inf. Model. 55(8): 1747-1756 (2015) - [j62]Matthias Hilbig, Matthias Rarey:
MONA 2: A Light Cheminformatics Platform for Interactive Compound Library Processing. J. Chem. Inf. Model. 55(10): 2071-2078 (2015) - 2014
- [j61]Angela M. Henzler, Sascha Urbaczek, Matthias Hilbig, Matthias Rarey:
An integrated approach to knowledge-driven structure-based virtual screening. J. Comput. Aided Mol. Des. 28(9): 927-939 (2014) - [j60]Stefan Bietz, Sascha Urbaczek, Benjamin Schulz, Matthias Rarey:
Protoss: a holistic approach to predict tautomers and protonation states in protein-ligand complexes. J. Cheminformatics 6(1): 12 (2014) - [j59]Karen T. Schomburg, Matthias Rarey:
Facing the challenges of computational target prediction. J. Cheminformatics 6(S-1): 3 (2014) - [j58]Eva Vennmann, Nadine Schneider, Gudrun Lange, Matthias Rarey:
Elucidating protein-protein interactions using the HYDE scoring function. J. Cheminformatics 6(S-1): 36 (2014) - [j57]Katrin Stierand, Tim Harder, Lothar Wissler, Christian Lemmen, Matthias Rarey:
Accessing Open PHACTS: interactive exploration of compounds and targets from the semantic web. J. Cheminformatics 6(S-1): 52 (2014) - [j56]Sascha Urbaczek, Adrian Kolodzik, Matthias Rarey:
The Valence State Combination Model: A Generic Framework for Handling Tautomers and Protonation States. J. Chem. Inf. Model. 54(3): 756-766 (2014) - [j55]Karen Schomburg, Stefan Bietz, Hans Briem, Angela M. Henzler, Sascha Urbaczek, Matthias Rarey:
Facing the Challenges of Structure-Based Target Prediction by Inverse Virtual Screening. J. Chem. Inf. Model. 54(6): 1676-1686 (2014) - [j54]Karen Schomburg, Matthias Rarey:
Benchmark Data Sets for Structure-Based Computational Target Prediction. J. Chem. Inf. Model. 54(8): 2261-2274 (2014) - 2013
- [j53]Nadine Schneider, Gudrun Lange, Sally A. Hindle, Robert Klein, Matthias Rarey:
A consistent description of HYdrogen bond and DEhydration energies in protein-ligand complexes: methods behind the HYDE scoring function. J. Comput. Aided Mol. Des. 27(1): 15-29 (2013) - [j52]Matthias Wirth, Andrea Volkamer, Vincent Zoete, Friedrich Rippmann, Olivier Michielin, Matthias Rarey, Wolfgang H. B. Sauer:
Protein pocket and ligand shape comparison and its application in virtual screening. J. Comput. Aided Mol. Des. 27(6): 511-524 (2013) - [j51]Christin Schärfer, Tanja Schulz-Gasch, Matthias Rarey:
TorsionAnalyzer: exploring conformational space. J. Cheminformatics 5(S-1): 3 (2013) - [j50]Matthias Rarey, Adrian Kolodzik, Sascha Urbaczek:
Let's talk about rings. J. Cheminformatics 5(S-1): 8 (2013) - [j49]Lennart Heinzerling, Matthias Rarey:
Force-field-based minimizations of protein-ligand complexes in the blink of an eye. J. Cheminformatics 5(S-1): 14 (2013) - [j48]Matthias Hilbig, Sascha Urbaczek, Inken Groth, Stefan Heuser, Matthias Rarey:
MONA - Interactive manipulation of molecule collections. J. Cheminformatics 5: 38 (2013) - [j47]Sascha Urbaczek, Adrian Kolodzik, Inken Groth, Stefan Heuser, Matthias Rarey:
Reading PDB: Perception of Molecules from 3D Atomic Coordinates. J. Chem. Inf. Model. 53(1): 76-87 (2013) - [j46]Mathias M. von Behren, Andrea Volkamer, Angela M. Henzler, Karen Schomburg, Sascha Urbaczek, Matthias Rarey:
Fast Protein Binding Site Comparison via an Index-Based Screening Technology. J. Chem. Inf. Model. 53(2): 411-422 (2013) - [j45]Hans-Christian Ehrlich, Angela M. Henzler, Matthias Rarey:
Searching for Recursively Defined Generic Chemical Patterns in Nonenumerated Fragment Spaces. J. Chem. Inf. Model. 53(7): 1676-1688 (2013) - 2012
- [j44]Andrea Volkamer, Daniel Kuhn, Friedrich Rippmann, Matthias Rarey:
DoGSiteScorer: a web server for automatic binding site prediction, analysis and druggability assessment. Bioinform. 28(15): 2074-2075 (2012) - [j43]Matthias Rarey:
Some thoughts on the "A" in computer-aided molecular design. J. Comput. Aided Mol. Des. 26(1): 113-114 (2012) - [j42]Nadine Schneider, Sally A. Hindle, Gudrun Lange, Robert Klein, Jürgen Albrecht, Hans Briem, Kristin Beyer, Holger Claußen, Marcus Gastreich, Christian Lemmen, Matthias Rarey:
Substantial improvements in large-scale redocking and screening using the novel HYDE scoring function. J. Comput. Aided Mol. Des. 26(6): 701-723 (2012) - [j41]Lennart Heinzerling, Robert Klein, Matthias Rarey:
Fast force field-based optimization of protein-ligand complexes with graphics processor. J. Comput. Chem. 33(32): 2554-2565 (2012) - [j40]Matthias Hilbig, Matthias Rarey:
Aligning chemical structure diagrams with local search. J. Cheminformatics 4(S-1): 4 (2012) - [j39]Hans-Christian Ehrlich, Matthias Rarey:
Systematic benchmark of substructure search in molecular graphs - From Ullmann to VF2. J. Cheminformatics 4: 13 (2012) - [j38]Angela M. Henzler, Sascha Urbaczek, Benjamin Schulz, Matthias Rarey:
A flexible-hydrogen interaction model for protein-ligand docking. J. Cheminformatics 4(S-1): 14 (2012) - [j37]Christin Schärfer, Tanja Schulz-Gasch, Matthias Rarey:
Systematic search for pairwise dependencies of torsion angles. J. Cheminformatics 4(S-1): 36 (2012) - [j36]Andrea Volkamer, Daniel Kuhn, Thomas Grombacher, Friedrich Rippmann, Matthias Rarey:
Combining Global and Local Measures for Structure-Based Druggability Predictions. J. Chem. Inf. Model. 52(2): 360-372 (2012) - [j35]Uta F. Lessel, Bernd Wellenzohn, J. Robert Fischer, Matthias Rarey:
Design of Combinatorial Libraries for the Exploration of Virtual Hits from Fragment Space Searches with LoFT. J. Chem. Inf. Model. 52(2): 373-379 (2012) - [j34]Tanja Schulz-Gasch, Christin Schärfer, Wolfgang Guba, Matthias Rarey:
TFD: Torsion Fingerprints As a New Measure To Compare Small Molecule Conformations. J. Chem. Inf. Model. 52(6): 1499-1512 (2012) - [j33]Adrian Kolodzik, Sascha Urbaczek, Matthias Rarey:
Unique Ring Families: A Chemically Meaningful Description of Molecular Ring Topologies. J. Chem. Inf. Model. 52(8): 2013-2021 (2012) - [j32]Hans-Christian Ehrlich, Andrea Volkamer, Matthias Rarey:
Searching for Substructures in Fragment Spaces. J. Chem. Inf. Model. 52(12): 3181-3189 (2012) - 2011
- [j31]Tobias Lippert, Tanja Schulz-Gasch, Olivier Roche, Wolfgang Guba, Matthias Rarey:
De novo design by pharmacophore-based searches in fragment spaces. J. Comput. Aided Mol. Des. 25(10): 931-945 (2011) - [j30]Hans-Christian Ehrlich, Matthias Rarey:
Searching substructures in fragment spaces. J. Cheminformatics 3(S-1): 11 (2011) - [j29]Karen Schomburg, Hans-Christian Ehrlich, Katrin Stierand, Matthias Rarey:
Chemical pattern visualization in 2D - the SMARTSviewer. J. Cheminformatics 3(S-1): 12 (2011) - [j28]Stefan Bietz, Sascha Urbaczek, Matthias Rarey:
Hydrogen placement in protein-ligand complexes under consideration of tautomerism. J. Cheminformatics 3(S-1): 13 (2011) - [j27]Katrin Stierand, Matthias Rarey:
Consistent two-dimensional visualization of protein-ligand complex series. J. Cheminformatics 3: 21 (2011) - [j26]Nadine Schneider, Gudrun Lange, Robert Klein, Christian Lemmen, Matthias Rarey:
HYDEing the false positives - scoring for lead optimization. J. Cheminformatics 3(S-1): 29 (2011) - [j25]J. Robert Fischer, Uta F. Lessel, Matthias Rarey:
Improving Similarity-Driven Library Design: Customized Matching and Regioselective Feature Trees. J. Chem. Inf. Model. 51(9): 2156-2163 (2011) - [j24]Sascha Urbaczek, Adrian Kolodzik, J. Robert Fischer, Tobias Lippert, Stefan Heuser, Inken Groth, Tanja Schulz-Gasch, Matthias Rarey:
NAOMI: On the Almost Trivial Task of Reading Molecules from Different File formats. J. Chem. Inf. Model. 51(12): 3199-3207 (2011) - 2010
- [j23]Andrea Volkamer, Thomas Grombacher, Matthias Rarey:
Where are the boundaries? Automated pocket detection for druggability studies. J. Cheminformatics 2(S-1): 11 (2010) - [j22]Katrin Stierand, Matthias Rarey:
PoseView - molecular interaction patterns at a glance. J. Cheminformatics 2(S-1): 50 (2010) - [j21]J. Robert Fischer, Uta F. Lessel, Matthias Rarey:
LoFT: Similarity-Driven Multiobjective Focused Library Design. J. Chem. Inf. Model. 50(1): 1-21 (2010) - [j20]Karen Schomburg, Hans-Christian Ehrlich, Katrin Stierand, Matthias Rarey:
From Structure Diagrams to Visual Chemical Patterns. J. Chem. Inf. Model. 50(9): 1529-1535 (2010) - [j19]Andrea Volkamer, Axel Griewel, Thomas Grombacher, Matthias Rarey:
Analyzing the Topology of Active Sites: On the Prediction of Pockets and Subpockets. J. Chem. Inf. Model. 50(11): 2041-2052 (2010) - no results
2000 – 2009
- 2009
- [j18]Andrea Zaliani, Krisztina Boda, Thomas Seidel, Achim Herwig, Christof H. Schwab, Johann Gasteiger, Holger Claussen, Christian Lemmen, Jörg Degen, Juri Pärn, Matthias Rarey:
Second-generation de novo design: a view from a medicinal chemist perspective. J. Comput. Aided Mol. Des. 23(8): 593-602 (2009) - [j17]Tobias Lippert, Matthias Rarey:
Fast automated placement of polar hydrogen atoms in protein-ligand complexes. J. Cheminformatics 1: 13 (2009) - [j16]Jochen Schlosser, Matthias Rarey:
Beyond the Virtual Screening Paradigm: Structure-Based Searching for New Lead Compounds. J. Chem. Inf. Model. 49(4): 800-809 (2009) - [j15]Axel Griewel, Ole Kayser, Jochen Schlosser, Matthias Rarey:
Conformational Sampling for Large-Scale Virtual Screening: Accuracy versus Ensemble Size. J. Chem. Inf. Model. 49(10): 2303-2311 (2009) - 2007
- [j14]Ingo Schellhammer, Matthias Rarey:
TrixX: structure-based molecule indexing for large-scale virtual screening in sublinear time. J. Comput. Aided Mol. Des. 21(5): 223-238 (2007) - [j13]Juri Pärn, Jörg Degen, Matthias Rarey:
Exploring fragment spaces under multiple physicochemical constraints. J. Comput. Aided Mol. Des. 21(6): 327-340 (2007) - [j12]Patrick C. Maaß, Tanja Schulz-Gasch, Martin Stahl, Matthias Rarey:
Recore: A Fast and Versatile Method for Scaffold Hopping Based on Small Molecule Crystal Structure Conformations. J. Chem. Inf. Model. 47(2): 390-399 (2007) - [j11]J. Robert Fischer, Matthias Rarey:
SwiFT: An Index Structure for Reduced Graph Descriptors in Virtual Screening and Clustering. J. Chem. Inf. Model. 47(4): 1341-1353 (2007) - 2006
- [j10]Katrin Stierand, Patrick C. Maaß, Matthias Rarey:
Molecular complexes at a glance: automated generation of two-dimensional complex diagrams. Bioinform. 22(14): 1710-1716 (2006) - [j9]Andreas Kämper, Joannis Apostolakis, Matthias Rarey, Christel M. Marian, Thomas Lengauer:
Fully Automated Flexible Docking of Ligands into Flexible Synthetic Receptors Using Forward and Inverse Docking Strategies. J. Chem. Inf. Model. 46(2): 903-911 (2006) - 2005
- [c4]Axel Griewel, Matthias Rarey:
From greedy to branch & bound and back: Assessing optimization strategies for incremental construction molecular docking tools. German Conference on Bioinformatics 2005: 119-130 - [e1]Andrew E. Torda, Stefan Kurtz, Matthias Rarey:
Proceedings of the German Conference on Bioinformatics (GCB 2005), Hamburg, Germany, October 5-7, 2005. LNI P-71, GI 2005, ISBN 3-88579-400-4 [contents] - 2004
- [j8]Torsten Crass, Iris Antes, Rico Basekow, Peer Bork, Christian Buning, Maik Christensen, Holger Claussen, Christian Ebeling, Peter Ernst, Valérie Gailus-Durner, Karl-Heinz Glatting, Rolf Gohla, Frank Gößling, Korbinian Grote, Karsten R. Heidtke, Alexander Herrmann, Sean O'Keeffe, O. Kießlich, Sven Kolibal, Jan O. Korbel, Thomas Lengauer, Ines Liebich, Mark van der Linden, Hannes Luz, Kathrin Meissner, Christian von Mering, Heinz-Theodor Mevissen, Hans-Werner Mewes, Holger Michael, Martin Mokrejs, Tobias Müller, Heike Pospisil, Matthias Rarey, Jens G. Reich, Ralf Schneider, Dietmar Schomburg, Steffen Schulze-Kremer, Knut Schwarzer, Ingolf Sommer, Stephan Springstubbe, Sándor Suhai, Gnanasekaran Thoppae, Martin Vingron, Jens Warfsmann, Thomas Werner, Daniel Wetzler, Edgar Wingender, Ralf Zimmer:
The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources. Bioinform. 20(2): 268-270 (2004) - [j7]Patrick C. Fricker, Marcus Gastreich, Matthias Rarey:
Automated Drawing of Structural Molecular Formulas under Constraints. J. Chem. Inf. Model. 44(3): 1065-1078 (2004) - 2002
- [j6]Sally A. Hindle, Matthias Rarey, Christian Buning, Thomas Lengauer:
Flexible docking under pharmacophore type constraints. J. Comput. Aided Mol. Des. 16(2): 129-149 (2002) - [c3]Matthias Rarey:
Geometric Problems and Algorithms in Computer-Aided Molecular Design. GI Jahrestagung (Ergänzungsband) 2002: 61-62 - 2001
- [b2]Matthias Rarey:
Algorithmen für den computergestützten Wirkstoffentwurf. GMD research series 22, GMD 2001, ISBN 978-3-88457-405-8, pp. 1-62 - [j5]Matthias Rarey, Martin Stahl:
Similarity searching in large combinatorial chemistry spaces. J. Comput. Aided Mol. Des. 15(6): 497-520 (2001) - no results
1990 – 1999
- 1999
- [j4]Matthias Rarey, Bernd Kramer, Thomas Lengauer:
Docking of hydrophobic ligands with interaction-based matching algorithms. Bioinform. 15(3): 243-250 (1999) - 1998
- [j3]Matthias Rarey, J. Scott Dixon:
Feature trees: A new molecular similarity measure based on tree matching. J. Comput. Aided Mol. Des. 12(5): 471-490 (1998) - [c2]Matthias Rarey, Bernd Kramer, Thomas Lengauer:
Docking of hydrophobic ligands with interaction-based matching algorithms. German Conference on Bioinformatics 1998 - 1997
- [j2]Matthias Rarey, Bernd Kramer, Thomas Lengauer:
Multiple automatic base selection: Protein-ligand docking based on incremental construction without manual intervention. J. Comput. Aided Mol. Des. 11(4): 369-384 (1997) - 1996
- [b1]Matthias Rarey:
Rechnergestützte Vorhersage von Rezeptor-Ligand-Wechselwirkungen. GMD-Bericht 268, Oldenbourg 1996, ISBN 978-3-486-24010-8, pp. 1-149 - [j1]Matthias Rarey, Stephan Wefing, Thomas Lengauer:
Placement of medium-sized molecular fragments into active sites of proteins. J. Comput. Aided Mol. Des. 10(1): 41-54 (1996) - 1995
- [c1]Matthias Rarey, Bernd Kramer, Thomas Lengauer:
Time-Efficient Docking of Flexible Ligands into Active Sites of Proteins. ISMB 1995: 300-308 - no results
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