MAPOS: a computer program for organic synthesis design based on synthon model of organic chemistry. - Ludek Matyska; Jaroslav Koca (J. Chem. Inf. Comput. Sci., 1991)

D-CICADA : A Software for Confromational PES Elucidation on Network of Workstations. - Ludek Matyska; Jaroslav Koca (J. Comput. Chem., 1994)

Conformational Analysis and Flexibility of Carbohydrates Using the CICADA Approach with MM3. - Jaroslav Koca; Serge Pérez; Anne Imberty (J. Comput. Chem., 1995)

A Multidimensional Driver for Quantum Chemistry Program MOPAC. - Martin Cernohorský; Michal Kutý; Jaroslav Koca (Comput. Chem., 1997)

A Molecular Modeling Study of the Catalytic Mechanism of Haloalkane Dehalogenase: 1. Quantum Chemical Study of the First Reaction Step. - Jirí Damborský; Michal Kutý; Miroslav Nemec; Jaroslav Koca (J. Chem. Inf. Comput. Sci., 1997)

A Molecular Modeling Study of the Catalytic Mechanism of Haloalkane Dehalogenase. 2. Quantum Chemical Study of Complete Reaction Mechanism. - Michal Kutý; Jirí Damborský; Martin Prokop; Jaroslav Koca (J. Chem. Inf. Comput. Sci., 1998)

VADER: New Software for Exploring Interconversions on Potential Energy Surfaces. - Martin Cernohorský; Sofiane Kettou; Jaroslav Koca (J. Chem. Inf. Comput. Sci., 1999)

TRITON: in silico construction of protein mutants and prediction of their activities. - Martin Prokop; Jirí Damborský; Jaroslav Koca (Bioinform., 2000)

Stability of Complexes of Aromatic Amides with Bromide Anion: Quantitative Structure-Property Relationships. - Michal Cajan; Jirí Damborský; Ivan Stibor; Jaroslav Koca (J. Chem. Inf. Comput. Sci., 2000)

Coordination number of zinc ions in the phosphotriesterase active site by molecular dynamics and quantum mechanics. - Jaroslav Koca; Chang-Guo Zhan; Robert C. Rittenhouse; Rick L. Ornstein (J. Comput. Chem., 2003)

CAVER: a new tool to explore routes from protein clefts, pockets and cavities. - Martin Petrek; Michal Otyepka; Pavel Banás; Pavlína Kosinová; Jaroslav Koca; Jirí Damborský (BMC Bioinform., 2006)

Optimized and parallelized implementation of the electronegativity equalization method and the atom-bond electronegativity equalization method. - Radka Svobodová Vareková; Jaroslav Koca (J. Comput. Chem., 2006)

TRITON: a graphical tool for ligand-binding protein engineering. - Martin Prokop; Jan Adam; Zdenek Kríz; Michaela Wimmerová; Jaroslav Koca (Bioinform., 2008)

In Silico Mutagenesis and Docking Studies of Pseudomonas aeruginosa PA-IIL Lectin Predicting Binding Modes and Energies. - Jan Adam; Zdenek Kríz; Martin Prokop; Michaela Wimmerová; Jaroslav Koca (J. Chem. Inf. Model., 2008)

Software news and updates electronegativity equalization method: Parameterization and validation for organic molecules using the Merz-Kollman-Singh charge distribution scheme. - Zuzana Jirousková; Radka Svobodová Vareková; Jakub Vanek; Jaroslav Koca (J. Comput. Chem., 2009)

QSPR designer - a program to design and evaluate QSPR models. Case study on pKa prediction. - Ondrej Skrehota; Radka Svobodová Vareková; Stanislav Geidl; Michal Kudera; David Sehnal; Crina-Maria Ionescu; Jaroslav Koca (J. Cheminformatics, 2011)

Predicting pKa Values of Substituted Phenols from Atomic Charges: Comparison of Different Quantum Mechanical Methods and Charge Distribution Schemes. - Radka Svobodová Vareková; Stanislav Geidl; Crina-Maria Ionescu; Ondrej Skrehota; Michal Kudera; David Sehnal; Tomás Bouchal; Ruben Abagyan; Heinrich J. Huber; Jaroslav Koca (J. Chem. Inf. Model., 2011)

Computational prediction of monosaccharide binding free energies to lectins with linear interaction energy models. - Sushil Kumar Mishra; Johan Sund; Johan Åqvist; Jaroslav Koca (J. Comput. Chem., 2012)

Virtual screening and in silico design of novel inhibitors of bacterial lectins. - Jan Alán; Petr Kulhánek; Jaroslav Koca (J. Cheminformatics, 2012)

How the methodology of 3D structure preparation influences the quality of QSPR models? - Stanislav Geidl; Roman Beránek; Radka Svobodová Vareková; Tomás Bouchal; Miroslav Brumovský; Michal Kudera; Ondrej Skrehota; Jaroslav Koca (J. Cheminformatics, 2012)

Searching for tunnels of proteins - comparison of approaches and available software tools. - Deepti Jaiswal Kundu; Radka Svobodová Vareková; Crina-Maria Ionescu; David Sehnal; Jaroslav Koca (J. Cheminformatics, 2012)

SiteBinder - an improved approach for comparing multiple protein structural motifs. Case studies on biologically important motifs. - David Sehnal; Radka Svobodová Vareková; Heinrich J. Huber; Stanislav Geidl; Crina-Maria Ionescu; Michaela Wimmerová; Jaroslav Koca (J. Cheminformatics, 2012)

QSPR designer - employ your own descriptors in the automated QSAR modeling process. - Ondrej Skrehota; Radka Svobodová Vareková; Stanislav Geidl; Michal Kudera; David Sehnal; Crina-Maria Ionescu; Jan Zidek; Jaroslav Koca (J. Cheminformatics, 2012)

In Silico Mutagenesis and Docking Study of Ralstonia solanacearum RSL Lectin: Performance of Docking Software To Predict Saccharide Binding. - Sushil Kumar Mishra; Jan Adam; Michaela Wimmerová; Jaroslav Koca (J. Chem. Inf. Model., 2012)

SiteBinder: An Improved Approach for Comparing Multiple Protein Structural Motifs. - David Sehnal; Radka Svobodová Vareková; Heinrich J. Huber; Stanislav Geidl; Crina-Maria Ionescu; Michaela Wimmerová; Jaroslav Koca (J. Chem. Inf. Model., 2012)

MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels. - Karel Berka; Ondrej Hanák; David Sehnal; Pavel Banás; Veronika Navrátilová; Deepti Jaiswal Kundu; Crina-Maria Ionescu; Radka Svobodová Vareková; Jaroslav Koca; Michal Otyepka (Nucleic Acids Res., 2012)

Charge Profile Analysis Reveals That Activation of Pro-apoptotic Regulators Bax and Bak Relies on Charge Transfer Mediated Allosteric Regulation. - Crina-Maria Ionescu; Radka Svobodová Vareková; Jochen H. M. Prehn; Heinrich J. Huber; Jaroslav Koca (PLoS Comput. Biol., 2012)

MOLE 2.0: advanced approach for analysis of biomacromolecular channels. - David Sehnal; Radka Svobodová Vareková; Karel Berka; Lukás Pravda; Veronika Navrátilová; Pavel Banás; Crina-Maria Ionescu; Michal Otyepka; Jaroslav Koca (J. Cheminformatics, 2013)

Nemesis - a molecular modeling package. - Jakub Stepán; Petr Kulhánek; Milan Lenco; Zora Strelcová; Ales Krenek; Jaroslav Koca (J. Cheminformatics, 2013)

Predicting pKa values from EEM atomic charges. - Radka Svobodová Vareková; Stanislav Geidl; Crina-Maria Ionescu; Ondrej Skrehota; Tomás Bouchal; David Sehnal; Ruben Abagyan; Jaroslav Koca (J. Cheminformatics, 2013)

Rapid Calculation of Accurate Atomic Charges for Proteins via the Electronegativity Equalization Method. - Crina-Maria Ionescu; Stanislav Geidl; Radka Svobodová Vareková; Jaroslav Koca (J. Chem. Inf. Model., 2013)

Anatomy of enzyme channels. - Lukás Pravda; Karel Berka; Radka Svobodová Vareková; David Sehnal; Pavel Banás; Roman A. Laskowski; Jaroslav Koca; Michal Otyepka (BMC Bioinform., 2014)

Engineering the Pseudomonas aeruginosa II lectin: designing mutants with changed affinity and specificity. - Zdenek Kríz; Jan Adam; Jana Mrázková; Petros Zotos; Thomais Chatzipavlou; Michaela Wimmerová; Jaroslav Koca (J. Comput. Aided Mol. Des., 2014)

Empirical charges for chemoinformatics applications. - Tomás Bouchal; Radka Svobodová Vareková; Tomás Racek; Crina-Maria Ionescu; Stanislav Geidl; Ales Krenek; Jaroslav Koca (J. Cheminformatics, 2014)

QM quality atomic charges for proteins. - Stanislav Geidl; Crina-Maria Ionescu; Radka Svobodová Vareková; Jaroslav Koca (J. Cheminformatics, 2014)

Consistency of sugar structures and their annotation in the PDB. - Deepti Jaiswal Kundu; David Sehnal; Radka Svobodová Vareková; Crina-Maria Ionescu; Jaroslav Koca (J. Cheminformatics, 2014)

MotiveValidator: interactive web-based validation of ligand and residue structure in biomolecular complexes. - Radka Svobodová Vareková; Deepti Jaiswal Kundu; David Sehnal; Crina-Maria Ionescu; Stanislav Geidl; Lukás Pravda; Vladimír Horský; Michaela Wimmerová; Jaroslav Koca (Nucleic Acids Res., 2014)

High-quality and universal empirical atomic charges for chemoinformatics applications. - Stanislav Geidl; Tomás Bouchal; Tomás Racek; Radka Svobodová Vareková; Václav Hejret; Ales Krenek; Ruben Abagyan; Jaroslav Koca (J. Cheminformatics, 2015)

AtomicChargeCalculator: interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules. - Crina-Maria Ionescu; David Sehnal; Francesco L. Falginella; Purbaj Pant; Lukás Pravda; Tomás Bouchal; Radka Svobodová Vareková; Stanislav Geidl; Jaroslav Koca (J. Cheminformatics, 2015)

How Does the Methodology of 3D Structure Preparation Influence the Quality of pKa Prediction? - Stanislav Geidl; Radka Svobodová Vareková; Veronika Bendová; Lukás Petrusek; Crina-Maria Ionescu; Zdenek Jurka; Ruben Abagyan; Jaroslav Koca (J. Chem. Inf. Model., 2015)

PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank. - David Sehnal; Lukás Pravda; Radka Svobodová Vareková; Crina-Maria Ionescu; Jaroslav Koca (Nucleic Acids Res., 2015)

ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank. - David Sehnal; Radka Svobodová Vareková; Lukás Pravda; Crina-Maria Ionescu; Stanislav Geidl; Vladimír Horský; Deepti Jaiswal Kundu; Michaela Wimmerová; Jaroslav Koca (Nucleic Acids Res., 2015)

Stepwise Catalytic Mechanism via Short-Lived Intermediate Inferred from Combined QM/MM MERP and PES Calculations on Retaining Glycosyltransferase ppGalNAcT2. - Tomás Trnka; Stanislav Kozmon; Igor Tvaroska; Jaroslav Koca (PLoS Comput. Biol., 2015)

NEEMP: software for validation, accurate calculation and fast parameterization of EEM charges. - Tomás Racek; Jana Pazúriková; Radka Svobodová Vareková; Stanislav Geidl; Ales Krenek; Francesco L. Falginella; Vladimír Horský; Václav Hejret; Jaroslav Koca (J. Cheminformatics, 2016)

CrocoBLAST: Running BLAST efficiently in the age of next-generation sequencing. - Ravi José Tristão Ramos; Allan Cézar de Azevedo Martins; Gabrielle da Silva Delgado; Crina-Maria Ionescu; Turán Peter Ürményi; Rosane Silva; Jaroslav Koca (Bioinform., 2017)

Mol*: Towards a Common Library and Tools for Web Molecular Graphics. - David Sehnal; Alexander S. Rose; Jaroslav Koca; Stephen K. Burley; Sameer Velankar (MolVa@EuroVis, 2018)

MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update). - Lukás Pravda; David Sehnal; Dominik Tousek; Veronika Navrátilová; Václav Bazgier; Karel Berka; Radka Svobodová Vareková; Jaroslav Koca; Michal Otyepka (Nucleic Acids Res., 2018)

ChannelsDB: database of biomacromolecular tunnels and pores. - Lukás Pravda; David Sehnal; Radka Svobodová Vareková; Veronika Navrátilová; Dominik Tousek; Karel Berka; Michal Otyepka; Jaroslav Koca (Nucleic Acids Res., 2018)

ValTrendsDB: bringing Protein Data Bank validation information closer to the user. - Vladimír Horský; Veronika Bendová; Dominik Tousek; Jaroslav Koca; Radka Svobodová Vareková (Bioinform., 2019)

PDBe: improved findability of macromolecular structure data in the PDB. - 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; et al. (Nucleic Acids Res., 2020)

Atomic Charge Calculator II: web-based tool for the calculation of partial atomic charges. - Tomás Racek; Ondrej Schindler; Dominik Tousek; Vladimír Horský; Karel Berka; Jaroslav Koca; Radka Svobodová Vareková (Nucleic Acids Res., 2020)

PDBe-KB: a community-driven resource for structural and functional annotations. - 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; et al. (Nucleic Acids Res., 2020)

BinaryCIF and CIFTools - Lightweight, efficient and extensible macromolecular data management. - David Sehnal; Sebastian Bittrich; Sameer Velankar; Jaroslav Koca; Radka Svobodová Vareková; Stephen K. Burley; Alexander S. Rose (PLoS Comput. Biol., 2020)

Optimized SQE atomic charges for peptides accessible via a web application. - Ondrej Schindler; Tomás Racek; Aleksandra Marsavelski; Jaroslav Koca; Karel Berka; Radka Svobodová Vareková (J. Cheminformatics, 2021)

Correction to: Optimized SQE atomic charges for peptides accessible via a web application. - Ondrej Schindler; Tomás Racek; Aleksandra Marsavelski; Jaroslav Koca; Karel Berka; Radka Svobodová Vareková (J. Cheminformatics, 2021)

Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures. - David Sehnal; Sebastian Bittrich; Mandar S. Deshpande; Radka Svobodová Vareková; Karel Berka; Václav Bazgier; Sameer Velankar; Stephen K. Burley; Jaroslav Koca; Alexander S. Rose (Nucleic Acids Res., 2021)