Jaroslav Koca

Publication Activity (10 Years)

Years Active: 1991-2021
Publications (10 Years): 13

Top Topics

Structural Patterns

Top Venues

J. Cheminformatics

Nucleic Acids Res.

J. Chem. Inf. Model.

Publications

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) (2021)
David Sehnal, Sebastian Bittrich, Mandar S. Deshpande, Radka Svobodová, 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) (2021)
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) (2021)
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) (2020)
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)
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) (2020)
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) (2020)
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) (2019)
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)
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) (2018)
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) (2018)
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) (2017)
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) (2016)
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) (2015)
Stanislav Geidl, Radka Svobodová Vareková, Veronika Bendová, Lukás Petrusek, Crina-Maria Ionescu, Zdenek Jurka, Ruben Abagyan, Jaroslav Koca
Prediction? J. Chem. Inf. Model. 55 (6) (2015)
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)
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) (2015)
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 (2015)
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 (2015)
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) (2014)
Stanislav Geidl, Crina-Maria Ionescu, Radka Svobodová Vareková, Jaroslav Koca
QM quality atomic charges for proteins. J. Cheminformatics 6 (S-1) (2014)
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 (2014)
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) (2014)
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) (2014)
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) (2014)
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 (2013)
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) (2013)
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 (2013)
Jakub Stepán, Petr Kulhánek, Milan Lenco, Zora Strelcová, Ales Krenek, Jaroslav Koca
Nemesis - a molecular modeling package. J. Cheminformatics 5 (S-1) (2013)
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) (2012)
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) (2012)
Sushil Kumar Mishra, Jan Adam, Michaela Wimmerová, Jaroslav Koca
RSL Lectin: Performance of Docking Software To Predict Saccharide Binding. J. Chem. Inf. Model. 52 (5) (2012)
Jan Alán, Petr Kulhánek, Jaroslav Koca
Virtual screening and in silico design of novel inhibitors of bacterial lectins. J. Cheminformatics 4 (S-1) (2012)
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) (2012)
Karel Berka, Ondrej Hanák, David Sehnal, Pavel Banás, Veronika Navrátilová, Deepti Jaiswal Kundu, Crina-Maria Ionescu, Radka Svobodová Vareková, Jaroslav Koca, Michal Otyepka
2.0: interactive web-based analysis of biomacromolecular channels. Nucleic Acids Res. 40 (Web-Server-Issue) (2012)
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) (2012)
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) (2012)
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) (2012)
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)
Ondrej Skrehota, Radka Svobodová Vareková, Stanislav Geidl, Michal Kudera, David Sehnal, Crina-Maria Ionescu, Jaroslav Koca
prediction. J. Cheminformatics 3 (S-1) (2011)
Radka Svobodová Vareková, Stanislav Geidl, Crina-Maria Ionescu, Ondrej Skrehota, Michal Kudera, David Sehnal, Tomás Bouchal, Ruben Abagyan, Heinrich J. Huber, Jaroslav Koca
Values of Substituted Phenols from Atomic Charges: Comparison of Different Quantum Mechanical Methods and Charge Distribution Schemes. J. Chem. Inf. Model. 51 (8) (2011)
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) (2009)
Jan Adam, Zdenek Kríz, Martin Prokop, Michaela Wimmerová, Jaroslav Koca
PA-IIL Lectin Predicting Binding Modes and Energies. J. Chem. Inf. Model. 48 (11) (2008)
Martin Prokop, Jan Adam, Zdenek Kríz, Michaela Wimmerová, Jaroslav Koca
TRITON: a graphical tool for ligand-binding protein engineering. Bioinform. 24 (17) (2008)
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) (2006)
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 (2006)
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) (2003)
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) (2000)
Martin Prokop, Jirí Damborský, Jaroslav Koca
TRITON: in silico construction of protein mutants and prediction of their activities. Bioinform. 16 (9) (2000)
Martin Cernohorský, Sofiane Kettou, Jaroslav Koca
VADER: New Software for Exploring Interconversions on Potential Energy Surfaces. J. Chem. Inf. Comput. Sci. 39 (4) (1999)
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) (1998)
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) (1997)
Martin Cernohorský, Michal Kutý, Jaroslav Koca
A Multidimensional Driver for Quantum Chemistry Program MOPAC. Comput. Chem. 21 (1) (1997)
Jaroslav Koca, Serge Pérez, Anne Imberty
Conformational Analysis and Flexibility of Carbohydrates Using the CICADA Approach with MM3. J. Comput. Chem. 16 (3) (1995)
Ludek Matyska, Jaroslav Koca
D-CICADA : A Software for Confromational PES Elucidation on Network of Workstations. J. Comput. Chem. 15 (9) (1994)
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) (1991)