Jaroslav Koca - RankMe

55 papers Journal 54Unranked 1

Year	Rank	Type	Title / Venue / Authors
2021	J	`jnl`	Correction to: Optimized SQE atomic charges for peptides accessible via a web application. J. Cheminformatics Ondrej Schindler, Tomás Racek, Aleksandra Marsavelski, Jaroslav Koca, Karel Berka, Radka Svobodová Vareková
2021	J	`jnl`	Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures. Nucleic Acids Res. David Sehnal, Sebastian Bittrich, Mandar S. Deshpande, Radka Svobodová Vareková, Karel Berka, Václav Bazgier, Sameer Velankar, Stephen K. Burley, Jaroslav Koca, Alexander S. Rose
2021	J	`jnl`	Optimized SQE atomic charges for peptides accessible via a web application. J. Cheminformatics Ondrej Schindler, Tomás Racek, Aleksandra Marsavelski, Jaroslav Koca, Karel Berka, Radka Svobodová Vareková
2020	J	`jnl`	Atomic Charge Calculator II: web-based tool for the calculation of partial atomic charges. Nucleic Acids Res. Tomás Racek, Ondrej Schindler, Dominik Tousek, Vladimír Horský, Karel Berka, Jaroslav Koca, Radka Svobodová Vareková
2020	J	`jnl`	BinaryCIF and CIFTools - Lightweight, efficient and extensible macromolecular data management. PLoS Comput. Biol. David Sehnal, Sebastian Bittrich, Sameer Velankar, Jaroslav Koca, Radka Svobodová Vareková, Stephen K. Burley, Alexander S. Rose
2020	J	`jnl`	PDBe-KB: a community-driven resource for structural and functional annotations. Nucleic Acids Res. 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
2020	J	`jnl`	PDBe: improved findability of macromolecular structure data in the PDB. Nucleic Acids Res. 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
2019	J	`jnl`	ValTrendsDB: bringing Protein Data Bank validation information closer to the user. Bioinform. Vladimír Horský, Veronika Bendová, Dominik Tousek, Jaroslav Koca, Radka Svobodová Vareková
2018	J	`jnl`	ChannelsDB: database of biomacromolecular tunnels and pores. Nucleic Acids Res. Lukás Pravda, David Sehnal, Radka Svobodová Vareková, Veronika Navrátilová, Dominik Tousek, Karel Berka, Michal Otyepka, Jaroslav Koca
2018	J	`jnl`	MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update). Nucleic Acids Res. Lukás Pravda, David Sehnal, Dominik Tousek, Veronika Navrátilová, Václav Bazgier, Karel Berka, Radka Svobodová Vareková, Jaroslav Koca, Michal Otyepka
2018	—	`conf`	Mol*: Towards a Common Library and Tools for Web Molecular Graphics. MolVa@EuroVis David Sehnal, Alexander S. Rose, Jaroslav Koca, Stephen K. Burley, Sameer Velankar
2017	J	`jnl`	CrocoBLAST: Running BLAST efficiently in the age of next-generation sequencing. Bioinform. Ravi José Tristão Ramos, Allan Cézar de Azevedo Martins, Gabrielle da Silva Delgado, Crina-Maria Ionescu, Turán Peter Ürményi, Rosane Silva, Jaroslav Koca
2016	J	`jnl`	NEEMP: software for validation, accurate calculation and fast parameterization of EEM charges. J. Cheminformatics Tomás Racek, Jana Pazúriková, Radka Svobodová Vareková, Stanislav Geidl, Ales Krenek, Francesco L. Falginella, Vladimír Horský, Václav Hejret, Jaroslav Koca
2015	J	`jnl`	AtomicChargeCalculator: interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules. J. Cheminformatics Crina-Maria Ionescu, David Sehnal, Francesco L. Falginella, Purbaj Pant, Lukás Pravda, Tomás Bouchal, Radka Svobodová Vareková, Stanislav Geidl, Jaroslav Koca
2015	J	`jnl`	High-quality and universal empirical atomic charges for chemoinformatics applications. J. Cheminformatics Stanislav Geidl, Tomás Bouchal, Tomás Racek, Radka Svobodová Vareková, Václav Hejret, Ales Krenek, Ruben Abagyan, Jaroslav Koca
2015	J	`jnl`	How Does the Methodology of 3D Structure Preparation Influence the Quality of p J. Chem. Inf. Model. Stanislav Geidl, Radka Svobodová Vareková, Veronika Bendová, Lukás Petrusek, Crina-Maria Ionescu, Zdenek Jurka, Ruben Abagyan, Jaroslav Koca
2015	J	`jnl`	PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank. Nucleic Acids Res. David Sehnal, Lukás Pravda, Radka Svobodová Vareková, Crina-Maria Ionescu, Jaroslav Koca
2015	J	`jnl`	Stepwise Catalytic Mechanism via Short-Lived Intermediate Inferred from Combined QM/MM MERP and PES Calculations on Retaining Glycosyltransferase ppGalNAcT2. PLoS Comput. Biol. Tomás Trnka, Stanislav Kozmon, Igor Tvaroska, Jaroslav Koca
2015	J	`jnl`	ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank. Nucleic Acids Res. David Sehnal, Radka Svobodová Vareková, Lukás Pravda, Crina-Maria Ionescu, Stanislav Geidl, Vladimír Horský, Deepti Jaiswal Kundu, Michaela Wimmerová, Jaroslav Koca
2014	J	`jnl`	Anatomy of enzyme channels. BMC Bioinform. Lukás Pravda, Karel Berka, Radka Svobodová Vareková, David Sehnal, Pavel Banás, Roman A. Laskowski, Jaroslav Koca, Michal Otyepka
2014	J	`jnl`	Consistency of sugar structures and their annotation in the PDB. J. Cheminformatics Deepti Jaiswal Kundu, David Sehnal, Radka Svobodová Vareková, Crina-Maria Ionescu, Jaroslav Koca
2014	J	`jnl`	Empirical charges for chemoinformatics applications. J. Cheminformatics Tomás Bouchal, Radka Svobodová Vareková, Tomás Racek, Crina-Maria Ionescu, Stanislav Geidl, Ales Krenek, Jaroslav Koca
2014	J	`jnl`	Engineering the Pseudomonas aeruginosa II lectin: designing mutants with changed affinity and specificity. J. Comput. Aided Mol. Des. Zdenek Kríz, Jan Adam, Jana Mrázková, Petros Zotos, Thomais Chatzipavlou, Michaela Wimmerová, Jaroslav Koca
2014	J	`jnl`	MotiveValidator: interactive web-based validation of ligand and residue structure in biomolecular complexes. Nucleic Acids Res. Radka Svobodová Vareková, Deepti Jaiswal Kundu, David Sehnal, Crina-Maria Ionescu, Stanislav Geidl, Lukás Pravda, Vladimír Horský, Michaela Wimmerová, Jaroslav Koca
2014	J	`jnl`	QM quality atomic charges for proteins. J. Cheminformatics Stanislav Geidl, Crina-Maria Ionescu, Radka Svobodová Vareková, Jaroslav Koca
2013	J	`jnl`	MOLE 2.0: advanced approach for analysis of biomacromolecular channels. J. Cheminformatics David Sehnal, Radka Svobodová Vareková, Karel Berka, Lukás Pravda, Veronika Navrátilová, Pavel Banás, Crina-Maria Ionescu, Michal Otyepka, Jaroslav Koca
2013	J	`jnl`	Nemesis - a molecular modeling package. J. Cheminformatics Jakub Stepán, Petr Kulhánek, Milan Lenco, Zora Strelcová, Ales Krenek, Jaroslav Koca
2013	J	`jnl`	Predicting pKa values from EEM atomic charges. J. Cheminformatics Radka Svobodová Vareková, Stanislav Geidl, Crina-Maria Ionescu, Ondrej Skrehota, Tomás Bouchal, David Sehnal, Ruben Abagyan, Jaroslav Koca
2013	J	`jnl`	Rapid Calculation of Accurate Atomic Charges for Proteins via the Electronegativity Equalization Method. J. Chem. Inf. Model. Crina-Maria Ionescu, Stanislav Geidl, Radka Svobodová Vareková, Jaroslav Koca
2012	J	`jnl`	Charge Profile Analysis Reveals That Activation of Pro-apoptotic Regulators Bax and Bak Relies on Charge Transfer Mediated Allosteric Regulation. PLoS Comput. Biol. Crina-Maria Ionescu, Radka Svobodová Vareková, Jochen H. M. Prehn, Heinrich J. Huber, Jaroslav Koca
2012	J	`jnl`	Computational prediction of monosaccharide binding free energies to lectins with linear interaction energy models. J. Comput. Chem. Sushil Kumar Mishra, Johan Sund, Johan Åqvist, Jaroslav Koca
2012	J	`jnl`	How the methodology of 3D structure preparation influences the quality of QSPR models? J. Cheminformatics Stanislav Geidl, Roman Beránek, Radka Svobodová Vareková, Tomás Bouchal, Miroslav Brumovský, Michal Kudera, Ondrej Skrehota, Jaroslav Koca
2012	J	`jnl`	In Silico Mutagenesis and Docking Study of J. Chem. Inf. Model. Sushil Kumar Mishra, Jan Adam, Michaela Wimmerová, Jaroslav Koca
2012	J	`jnl`	MOLE Nucleic Acids Res. Karel Berka, Ondrej Hanák, David Sehnal, Pavel Banás, Veronika Navrátilová, Deepti Jaiswal Kundu, Crina-Maria Ionescu, Radka Svobodová Vareková, Jaroslav Koca, Michal Otyepka
2012	J	`jnl`	QSPR designer - employ your own descriptors in the automated QSAR modeling process. J. Cheminformatics Ondrej Skrehota, Radka Svobodová Vareková, Stanislav Geidl, Michal Kudera, David Sehnal, Crina-Maria Ionescu, Jan Zidek, Jaroslav Koca
2012	J	`jnl`	Searching for tunnels of proteins - comparison of approaches and available software tools. J. Cheminformatics Deepti Jaiswal Kundu, Radka Svobodová Vareková, Crina-Maria Ionescu, David Sehnal, Jaroslav Koca
2012	J	`jnl`	SiteBinder - an improved approach for comparing multiple protein structural motifs. Case studies on biologically important motifs. J. Cheminformatics David Sehnal, Radka Svobodová Vareková, Heinrich J. Huber, Stanislav Geidl, Crina-Maria Ionescu, Michaela Wimmerová, Jaroslav Koca
2012	J	`jnl`	SiteBinder: An Improved Approach for Comparing Multiple Protein Structural Motifs. J. Chem. Inf. Model. David Sehnal, Radka Svobodová Vareková, Heinrich J. Huber, Stanislav Geidl, Crina-Maria Ionescu, Michaela Wimmerová, Jaroslav Koca
2012	J	`jnl`	Virtual screening and in silico design of novel inhibitors of bacterial lectins. J. Cheminformatics Jan Alán, Petr Kulhánek, Jaroslav Koca
2011	J	`jnl`	Predicting p J. Chem. Inf. Model. Radka Svobodová Vareková, Stanislav Geidl, Crina-Maria Ionescu, Ondrej Skrehota, Michal Kudera, David Sehnal, Tomás Bouchal, Ruben Abagyan, Heinrich J. Huber, Jaroslav Koca
2011	J	`jnl`	QSPR designer - a program to design and evaluate QSPR models. Case study on pK J. Cheminformatics Ondrej Skrehota, Radka Svobodová Vareková, Stanislav Geidl, Michal Kudera, David Sehnal, Crina-Maria Ionescu, Jaroslav Koca
2009	J	`jnl`	Software news and updates electronegativity equalization method: Parameterization and validation for organic molecules using the Merz-Kollman-Singh charge distribution scheme. J. Comput. Chem. Zuzana Jirousková, Radka Svobodová Vareková, Jakub Vanek, Jaroslav Koca
2008	J	`jnl`	TRITON: a graphical tool for ligand-binding protein engineering. Bioinform. Martin Prokop, Jan Adam, Zdenek Kríz, Michaela Wimmerová, Jaroslav Koca
2006	J	`jnl`	CAVER: a new tool to explore routes from protein clefts, pockets and cavities. BMC Bioinform. Martin Petrek, Michal Otyepka, Pavel Banás, Pavlína Kosinová, Jaroslav Koca, Jirí Damborský
2006	J	`jnl`	Optimized and parallelized implementation of the electronegativity equalization method and the atom-bond electronegativity equalization method. J. Comput. Chem. Radka Svobodová Vareková, Jaroslav Koca
2003	J	`jnl`	Coordination number of zinc ions in the phosphotriesterase active site by molecular dynamics and quantum mechanics. J. Comput. Chem. Jaroslav Koca, Chang-Guo Zhan, Robert C. Rittenhouse, Rick L. Ornstein
2000	J	`jnl`	Stability of Complexes of Aromatic Amides with Bromide Anion: Quantitative Structure-Property Relationships. J. Chem. Inf. Comput. Sci. Michal Cajan, Jirí Damborský, Ivan Stibor, Jaroslav Koca
2000	J	`jnl`	TRITON: in silico construction of protein mutants and prediction of their activities. Bioinform. Martin Prokop, Jirí Damborský, Jaroslav Koca
1999	J	`jnl`	VADER: New Software for Exploring Interconversions on Potential Energy Surfaces. J. Chem. Inf. Comput. Sci. Martin Cernohorský, Sofiane Kettou, Jaroslav Koca
1998	J	`jnl`	A Molecular Modeling Study of the Catalytic Mechanism of Haloalkane Dehalogenase. 2. Quantum Chemical Study of Complete Reaction Mechanism. J. Chem. Inf. Comput. Sci. Michal Kutý, Jirí Damborský, Martin Prokop, Jaroslav Koca
1997	J	`jnl`	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. Jirí Damborský, Michal Kutý, Miroslav Nemec, Jaroslav Koca
1997	J	`jnl`	A Multidimensional Driver for Quantum Chemistry Program MOPAC. Comput. Chem. Martin Cernohorský, Michal Kutý, Jaroslav Koca
1995	J	`jnl`	Conformational Analysis and Flexibility of Carbohydrates Using the CICADA Approach with MM3. J. Comput. Chem. Jaroslav Koca, Serge Pérez, Anne Imberty
1994	J	`jnl`	D-CICADA : A Software for Confromational PES Elucidation on Network of Workstations. J. Comput. Chem. Ludek Matyska, Jaroslav Koca
1991	J	`jnl`	MAPOS: a computer program for organic synthesis design based on synthon model of organic chemistry. J. Chem. Inf. Comput. Sci. Ludek Matyska, Jaroslav Koca