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Jaroslav Koca
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2020 – today
- 2021
- [j55]Ondrej Schindler
, Tomás Racek
, Aleksandra Marsavelski
, Jaroslav Koca, Karel Berka
, Radka Svobodová Vareková
:
Optimized SQE atomic charges for peptides accessible via a web application. J. Cheminformatics 13(1): 45 (2021) - [j54]Ondrej Schindler
, Tomás Racek, Aleksandra Marsavelski, Jaroslav Koca, Karel Berka
, Radka Svobodová Vareková
:
Correction to: Optimized SQE atomic charges for peptides accessible via a web application. J. Cheminformatics 13(1): 52 (2021) - [j53]David Sehnal
, Sebastian Bittrich
, Mandar S. Deshpande
, Radka Svobodová Vareková
, Karel Berka
, Václav Bazgier
, Sameer Velankar
, Stephen K. Burley
, Jaroslav Koca
, Alexander S. Rose
:
Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures. Nucleic Acids Res. 49(Webserver-Issue): 431-437 (2021) - 2020
- [j52]David R. Armstrong
, John M. Berrisford
, Matthew J. Conroy
, Aleksandras Gutmanas
, Stephen Anyango
, Preeti Choudhary
, Alice R. Clark
, Jose M. Dana, Mandar S. Deshpande
, Roisin Dunlop, Paul J. Gane, Romana Gáborová, Deepti Gupta
, Pauline Haslam, Jaroslav Koca, Lora Mak
, Saqib Mir
, Abhik Mukhopadhyay, Nurul Nadzirin, Sreenath Nair
, Typhaine Paysan-Lafosse
, Lukás Pravda
, David Sehnal, Osman Salih
, Oliver S. Smart, James Tolchard
, Mihaly Varadi
, Radka Svobodová Vareková
, Hossam Zaki
, Gerard J. Kleywegt
, Sameer Velankar
:
PDBe: improved findability of macromolecular structure data in the PDB. Nucleic Acids Res. 48(Database-Issue): D335-D343 (2020) - [j51]Mihaly Varadi
, John M. Berrisford, Mandar S. Deshpande
, Sreenath Nair
, Aleksandras Gutmanas
, David R. Armstrong
, Lukás Pravda
, Bissan Al-Lazikani
, Stephen Anyango
, Geoffrey J. Barton, Karel Berka
, Tom L. Blundell, Neera Borkakoti
, Jose M. Dana, Sayoni Das, Sucharita Dey, Patrizio Di Micco, Franca Fraternali
, Toby J. Gibson
, Manuela Helmer-Citterich, David Hoksza, Liang-Chin Huang, Rishabh Jain, Harry Jubb, Christos C. Kannas
, Natarajan Kannan, Jaroslav Koca, Radoslav Krivák, Manjeet Kumar
, Emmanuel D. Levy, Fábio Madeira
, M. S. Madhusudhan, Henry J. Martell
, Stuart A. MacGowan
, Jake E. McGreig
, Saqib Mir, Abhik Mukhopadhyay, Luca Parca
, Typhaine Paysan-Lafosse
, Leandro G. Radusky, António J. M. Ribeiro
, Luis Serrano, Ian Sillitoe, Gulzar Singh, Petr Skoda
, Radka Svobodová Vareková
, Jonathan D. Tyzack
, Alfonso Valencia, Eloy D. Villasclaras-Fernández, Wim F. Vranken, Mark N. Wass, Janet M. Thornton
, Michael J. E. Sternberg
, Christine A. Orengo, Sameer Velankar
:
PDBe-KB: a community-driven resource for structural and functional annotations. Nucleic Acids Res. 48(Database-Issue): D344-D353 (2020) - [j50]Tomás Racek
, Ondrej Schindler
, Dominik Tousek, Vladimír Horský
, Karel Berka
, Jaroslav Koca, Radka Svobodová Vareková
:
Atomic Charge Calculator II: web-based tool for the calculation of partial atomic charges. Nucleic Acids Res. 48(Webserver-Issue): W591-W596 (2020) - [j49]David Sehnal, Sebastian Bittrich
, Sameer Velankar
, Jaroslav Koca
, Radka Svobodová Vareková
, Stephen K. Burley, Alexander S. Rose
:
BinaryCIF and CIFTools - Lightweight, efficient and extensible macromolecular data management. PLoS Comput. Biol. 16(10) (2020)
2010 – 2019
- 2019
- [j48]Vladimír Horský
, Veronika Bendová, Dominik Tousek, Jaroslav Koca, Radka Svobodová Vareková
:
ValTrendsDB: bringing Protein Data Bank validation information closer to the user. Bioinform. 35(24): 5389-5390 (2019) - 2018
- [j47]Lukás Pravda
, David Sehnal, Radka Svobodová Vareková
, Veronika Navrátilová, Dominik Tousek, Karel Berka
, Michal Otyepka
, Jaroslav Koca
:
ChannelsDB: database of biomacromolecular tunnels and pores. Nucleic Acids Res. 46(Database-Issue): D399-D405 (2018) - [j46]Lukás Pravda
, David Sehnal, Dominik Tousek, Veronika Navrátilová, Václav Bazgier, Karel Berka
, Radka Svobodová Vareková
, Jaroslav Koca, Michal Otyepka
:
MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update). Nucleic Acids Res. 46(Webserver-Issue): W368-W373 (2018) - [c1]David Sehnal, Alexander S. Rose
, Jaroslav Koca, Stephen K. Burley, Sameer Velankar:
Mol*: Towards a Common Library and Tools for Web Molecular Graphics. MolVa@EuroVis 2018: 29-33 - 2017
- [j45]Ravi José Tristão Ramos, Allan Cézar de Azevedo Martins
, Gabrielle da Silva Delgado, Crina-Maria Ionescu, Turán Peter Ürményi, Rosane Silva
, Jaroslav Koca
:
CrocoBLAST: Running BLAST efficiently in the age of next-generation sequencing. Bioinform. 33(22): 3648-3651 (2017) - 2016
- [j44]Tomás Racek
, Jana Pazúriková, Radka Svobodová Vareková
, Stanislav Geidl, Ales Krenek
, Francesco L. Falginella, Vladimír Horský
, Václav Hejret, Jaroslav Koca
:
NEEMP: software for validation, accurate calculation and fast parameterization of EEM charges. J. Cheminformatics 8(1): 57:1-57:14 (2016) - 2015
- [j43]Crina-Maria Ionescu, David Sehnal
, Francesco L. Falginella, Purbaj Pant
, Lukás Pravda
, Tomás Bouchal, Radka Svobodová Vareková
, Stanislav Geidl, Jaroslav Koca
:
AtomicChargeCalculator: interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules. J. Cheminformatics 7: 50:1-50:13 (2015) - [j42]Stanislav Geidl, Tomás Bouchal, Tomás Racek
, Radka Svobodová Vareková
, Václav Hejret, Ales Krenek
, Ruben Abagyan, Jaroslav Koca
:
High-quality and universal empirical atomic charges for chemoinformatics applications. J. Cheminformatics 7: 59:1-59:10 (2015) - [j41]Stanislav Geidl, Radka Svobodová Vareková
, Veronika Bendová, Lukás Petrusek, Crina-Maria Ionescu, Zdenek Jurka, Ruben Abagyan, Jaroslav Koca
:
How Does the Methodology of 3D Structure Preparation Influence the Quality of pKa Prediction? J. Chem. Inf. Model. 55(6): 1088-1097 (2015) - [j40]David Sehnal
, Radka Svobodová Vareková
, Lukás Pravda
, Crina-Maria Ionescu, Stanislav Geidl, Vladimír Horský
, Deepti Jaiswal Kundu
, Michaela Wimmerová
, Jaroslav Koca
:
ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank. Nucleic Acids Res. 43(Database-Issue): 369-375 (2015) - [j39]David Sehnal
, Lukás Pravda
, Radka Svobodová Vareková
, Crina-Maria Ionescu, Jaroslav Koca
:
PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank. Nucleic Acids Res. 43(Webserver-Issue): W383-W388 (2015) - [j38]Tomás Trnka
, Stanislav Kozmon
, Igor Tvaroska
, Jaroslav Koca
:
Stepwise Catalytic Mechanism via Short-Lived Intermediate Inferred from Combined QM/MM MERP and PES Calculations on Retaining Glycosyltransferase ppGalNAcT2. PLoS Comput. Biol. 11(4) (2015) - 2014
- [j37]Lukás Pravda
, Karel Berka
, Radka Svobodová Vareková
, David Sehnal
, Pavel Banás, Roman A. Laskowski
, Jaroslav Koca
, Michal Otyepka
:
Anatomy of enzyme channels. BMC Bioinform. 15: 379 (2014) - [j36]Zdenek Kríz, Jan Adam, Jana Mrázková
, Petros Zotos, Thomais Chatzipavlou, Michaela Wimmerová
, Jaroslav Koca
:
Engineering the Pseudomonas aeruginosa II lectin: designing mutants with changed affinity and specificity. J. Comput. Aided Mol. Des. 28(9): 951-960 (2014) - [j35]Deepti Jaiswal Kundu
, David Sehnal, Radka Svobodová Vareková, Crina-Maria Ionescu, Jaroslav Koca:
Consistency of sugar structures and their annotation in the PDB. J. Cheminformatics 6(S-1): 41 (2014) - [j34]Tomás Bouchal, Radka Svobodová Vareková, Tomás Racek, Crina-Maria Ionescu, Stanislav Geidl, Ales Krenek, Jaroslav Koca:
Empirical charges for chemoinformatics applications. J. Cheminformatics 6(S-1): 60 (2014) - [j33]Stanislav Geidl, Crina-Maria Ionescu, Radka Svobodová Vareková, Jaroslav Koca:
QM quality atomic charges for proteins. J. Cheminformatics 6(S-1): 61 (2014) - [j32]Radka Svobodová Vareková
, Deepti Jaiswal Kundu
, David Sehnal
, Crina-Maria Ionescu, Stanislav Geidl, Lukás Pravda
, Vladimír Horský
, Michaela Wimmerová
, Jaroslav Koca
:
MotiveValidator: interactive web-based validation of ligand and residue structure in biomolecular complexes. Nucleic Acids Res. 42(Webserver-Issue): 227-233 (2014) - 2013
- [j31]Jakub Stepán, Petr Kulhánek, Milan Lenco, Zora Strelcová, Ales Krenek, Jaroslav Koca:
Nemesis - a molecular modeling package. J. Cheminformatics 5(S-1): 12 (2013) - [j30]Radka Svobodová Vareková
, Stanislav Geidl, Crina-Maria Ionescu, Ondrej Skrehota, Tomás Bouchal, David Sehnal
, Ruben Abagyan, Jaroslav Koca
:
Predicting pKa values from EEM atomic charges. J. Cheminformatics 5: 18 (2013) - [j29]David Sehnal, Radka Svobodová Vareková, Karel Berka, Lukás Pravda, Veronika Navrátilová, Pavel Banás, Crina-Maria Ionescu, Michal Otyepka, Jaroslav Koca:
MOLE 2.0: advanced approach for analysis of biomacromolecular channels. J. Cheminformatics 5: 39 (2013) - [j28]Crina-Maria Ionescu, Stanislav Geidl, Radka Svobodová Vareková
, Jaroslav Koca
:
Rapid Calculation of Accurate Atomic Charges for Proteins via the Electronegativity Equalization Method. J. Chem. Inf. Model. 53(10): 2548-2558 (2013) - 2012
- [j27]Sushil Kumar Mishra
, Johan Sund, Johan Åqvist, Jaroslav Koca
:
Computational prediction of monosaccharide binding free energies to lectins with linear interaction energy models. J. Comput. Chem. 33(29): 2340-2350 (2012) - [j26]Jan Alán, Petr Kulhánek, Jaroslav Koca:
Virtual screening and in silico design of novel inhibitors of bacterial lectins. J. Cheminformatics 4(S-1): 1 (2012) - [j25]Ondrej Skrehota, Radka Svobodová Vareková, Stanislav Geidl, Michal Kudera, David Sehnal, Crina-Maria Ionescu, Jan Zidek, Jaroslav Koca:
QSPR designer - employ your own descriptors in the automated QSAR modeling process. J. Cheminformatics 4(S-1): 37 (2012) - [j24]David Sehnal, Radka Svobodová Vareková, Heinrich J. Huber, Stanislav Geidl, Crina-Maria Ionescu, Michaela Wimmerová
, Jaroslav Koca:
SiteBinder - an improved approach for comparing multiple protein structural motifs. Case studies on biologically important motifs. J. Cheminformatics 4(S-1): 59 (2012) - [j23]Deepti Jaiswal Kundu, Radka Svobodová Vareková, Crina-Maria Ionescu, David Sehnal, Jaroslav Koca:
Searching for tunnels of proteins - comparison of approaches and available software tools. J. Cheminformatics 4(S-1): 60 (2012) - [j22]Stanislav Geidl, Roman Beránek, Radka Svobodová Vareková, Tomás Bouchal, Miroslav Brumovský, Michal Kudera, Ondrej Skrehota, Jaroslav Koca:
How the methodology of 3D structure preparation influences the quality of QSPR models? J. Cheminformatics 4(S-1): 61 (2012) - [j21]David Sehnal
, Radka Svobodová Vareková
, Heinrich J. Huber, Stanislav Geidl, Crina-Maria Ionescu, Michaela Wimmerová
, Jaroslav Koca
:
SiteBinder: An Improved Approach for Comparing Multiple Protein Structural Motifs. J. Chem. Inf. Model. 52(2): 343-359 (2012) - [j20]Sushil Kumar Mishra
, Jan Adam, Michaela Wimmerová
, Jaroslav Koca
:
In Silico Mutagenesis and Docking Study of Ralstonia solanacearum RSL Lectin: Performance of Docking Software To Predict Saccharide Binding. J. Chem. Inf. Model. 52(5): 1250-1261 (2012) - [j19]Karel Berka
, Ondrej Hanák, David Sehnal
, Pavel Banás, Veronika Navrátilová, Deepti Jaiswal Kundu
, Crina-Maria Ionescu, Radka Svobodová Vareková
, Jaroslav Koca
, Michal Otyepka
:
MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels. Nucleic Acids Res. 40(Web-Server-Issue): 222-227 (2012) - [j18]Crina-Maria Ionescu, Radka Svobodová Vareková
, Jochen H. M. Prehn
, Heinrich J. Huber, Jaroslav Koca
:
Charge Profile Analysis Reveals That Activation of Pro-apoptotic Regulators Bax and Bak Relies on Charge Transfer Mediated Allosteric Regulation. PLoS Comput. Biol. 8(6) (2012) - 2011
- [j17]Ondrej Skrehota, Radka Svobodová Vareková
, Stanislav Geidl, Michal Kudera, David Sehnal
, Crina-Maria Ionescu, Jaroslav Koca:
QSPR designer - a program to design and evaluate QSPR models. Case study on pKa prediction. J. Cheminformatics 3(S-1): 16 (2011) - [j16]Radka Svobodová Vareková
, Stanislav Geidl, Crina-Maria Ionescu, Ondrej Skrehota, Michal Kudera, David Sehnal
, Tomás Bouchal, Ruben Abagyan, Heinrich J. Huber, Jaroslav Koca
:
Predicting pKa Values of Substituted Phenols from Atomic Charges: Comparison of Different Quantum Mechanical Methods and Charge Distribution Schemes. J. Chem. Inf. Model. 51(8): 1795-1806 (2011)
2000 – 2009
- 2009
- [j15]Zuzana Jirousková, Radka Svobodová Vareková
, Jakub Vanek, Jaroslav Koca
:
Software news and updates electronegativity equalization method: Parameterization and validation for organic molecules using the Merz-Kollman-Singh charge distribution scheme. J. Comput. Chem. 30(7): 1174-1178 (2009) - 2008
- [j14]Martin Prokop, Jan Adam, Zdenek Kríz, Michaela Wimmerová
, Jaroslav Koca
:
TRITON: a graphical tool for ligand-binding protein engineering. Bioinform. 24(17): 1955-1956 (2008) - [j13]Jan Adam, Zdenek Kríz, Martin Prokop, Michaela Wimmerová
, Jaroslav Koca
:
In Silico Mutagenesis and Docking Studies of Pseudomonas aeruginosa PA-IIL Lectin Predicting Binding Modes and Energies. J. Chem. Inf. Model. 48(11): 2234-2242 (2008) - 2006
- [j12]Martin Petrek, Michal Otyepka
, Pavel Banás, Pavlína Kosinová, Jaroslav Koca
, Jirí Damborský
:
CAVER: a new tool to explore routes from protein clefts, pockets and cavities. BMC Bioinform. 7: 316 (2006) - [j11]Radka Svobodová Vareková
, Jaroslav Koca
:
Optimized and parallelized implementation of the electronegativity equalization method and the atom-bond electronegativity equalization method. J. Comput. Chem. 27(3): 396-405 (2006) - 2003
- [j10]Jaroslav Koca
, Chang-Guo Zhan, Robert C. Rittenhouse, Rick L. Ornstein:
Coordination number of zinc ions in the phosphotriesterase active site by molecular dynamics and quantum mechanics. J. Comput. Chem. 24(3): 368-378 (2003) - 2000
- [j9]Martin Prokop, Jirí Damborský
, Jaroslav Koca
:
TRITON: in silico construction of protein mutants and prediction of their activities. Bioinform. 16(9): 845-846 (2000) - [j8]Michal Cajan, Jirí Damborský
, Ivan Stibor, Jaroslav Koca
:
Stability of Complexes of Aromatic Amides with Bromide Anion: Quantitative Structure-Property Relationships. J. Chem. Inf. Comput. Sci. 40(5): 1151-1157 (2000)
1990 – 1999
- 1999
- [j7]Martin Cernohorský, Sofiane Kettou, Jaroslav Koca
:
VADER: New Software for Exploring Interconversions on Potential Energy Surfaces. J. Chem. Inf. Comput. Sci. 39(4): 705-712 (1999) - 1998
- [j6]Michal Kutý
, Jirí Damborský
, Martin Prokop, Jaroslav Koca
:
A Molecular Modeling Study of the Catalytic Mechanism of Haloalkane Dehalogenase. 2. Quantum Chemical Study of Complete Reaction Mechanism. J. Chem. Inf. Comput. Sci. 38(4): 736-741 (1998) - 1997
- [j5]Martin Cernohorský, Michal Kutý, Jaroslav Koca:
A Multidimensional Driver for Quantum Chemistry Program MOPAC. Comput. Chem. 21(1): 35-44 (1997) - [j4]Jirí Damborský
, Michal Kutý
, Miroslav Nemec, Jaroslav Koca
:
A Molecular Modeling Study of the Catalytic Mechanism of Haloalkane Dehalogenase: 1. Quantum Chemical Study of the First Reaction Step. J. Chem. Inf. Comput. Sci. 37(3): 562-568 (1997) - 1995
- [j3]Jaroslav Koca
, Serge Pérez, Anne Imberty:
Conformational Analysis and Flexibility of Carbohydrates Using the CICADA Approach with MM3. J. Comput. Chem. 16(3): 296-310 (1995) - 1994
- [j2]Ludek Matyska, Jaroslav Koca
:
D-CICADA : A Software for Confromational PES Elucidation on Network of Workstations. J. Comput. Chem. 15(9): 937-946 (1994) - 1991
- [j1]Ludek Matyska
, Jaroslav Koca
:
MAPOS: a computer program for organic synthesis design based on synthon model of organic chemistry. J. Chem. Inf. Comput. Sci. 31(3): 380-386 (1991)
Coauthor Index
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