Jaroslav Koca
Orcid: 0000-0002-2780-4901
According to our database1,
Jaroslav Koca
authored at least 56 papers
between 1991 and 2021.
Collaborative distances:
Collaborative distances:
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Online presence:
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on orcid.org
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on id.loc.gov
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Bibliography
2021
Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures.
Nucleic Acids Res., 2021
Correction to: Optimized SQE atomic charges for peptides accessible via a web application.
J. Cheminformatics, 2021
J. Cheminformatics, 2021
2020
BinaryCIF and CIFTools - Lightweight, efficient and extensible macromolecular data management.
PLoS Comput. Biol., 2020
Nucleic Acids Res., 2020
Atomic Charge Calculator II: web-based tool for the calculation of partial atomic charges.
Nucleic Acids Res., 2020
Nucleic Acids Res., 2020
2019
Bioinform., 2019
2018
Nucleic Acids Res., 2018
MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update).
Nucleic Acids Res., 2018
Proceedings of the 1st Workshop on Molecular Graphics and Visual Analysis of Molecular Data, 2018
2017
Bioinform., 2017
2016
NEEMP: software for validation, accurate calculation and fast parameterization of EEM charges.
J. Cheminformatics, 2016
2015
Stepwise Catalytic Mechanism via Short-Lived Intermediate Inferred from Combined QM/MM MERP and PES Calculations on Retaining Glycosyltransferase ppGalNAcT2.
PLoS Comput. Biol., 2015
ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank.
Nucleic Acids Res., 2015
PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank.
Nucleic Acids Res., 2015
How Does the Methodology of 3D Structure Preparation Influence the Quality of p<i>K</i><sub>a</sub> Prediction?
J. Chem. Inf. Model., 2015
AtomicChargeCalculator: interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules.
J. Cheminformatics, 2015
High-quality and universal empirical atomic charges for chemoinformatics applications.
J. Cheminformatics, 2015
2014
MotiveValidator: interactive web-based validation of ligand and residue structure in biomolecular complexes.
Nucleic Acids Res., 2014
J. Cheminformatics, 2014
Engineering the Pseudomonas aeruginosa II lectin: designing mutants with changed affinity and specificity.
J. Comput. Aided Mol. Des., 2014
2013
Rapid Calculation of Accurate Atomic Charges for Proteins via the Electronegativity Equalization Method.
J. Chem. Inf. Model., 2013
J. Cheminformatics, 2013
2012
Charge Profile Analysis Reveals That Activation of Pro-apoptotic Regulators Bax and Bak Relies on Charge Transfer Mediated Allosteric Regulation.
PLoS Comput. Biol., 2012
Nucleic Acids Res., 2012
J. Chem. Inf. Model., 2012
In Silico Mutagenesis and Docking Study of <i>Ralstonia solanacearum</i> RSL Lectin: Performance of Docking Software To Predict Saccharide Binding.
J. Chem. Inf. Model., 2012
J. Cheminformatics, 2012
SiteBinder - an improved approach for comparing multiple protein structural motifs. Case studies on biologically important motifs.
J. Cheminformatics, 2012
Searching for tunnels of proteins - comparison of approaches and available software tools.
J. Cheminformatics, 2012
How the methodology of 3D structure preparation influences the quality of QSPR models?
J. Cheminformatics, 2012
J. Cheminformatics, 2012
Computational prediction of monosaccharide binding free energies to lectins with linear interaction energy models.
J. Comput. Chem., 2012
2011
Predicting p<i>K</i><sub>a</sub> Values of Substituted Phenols from Atomic Charges: Comparison of Different Quantum Mechanical Methods and Charge Distribution Schemes.
J. Chem. Inf. Model., 2011
QSPR designer - a program to design and evaluate QSPR models. Case study on pK<sub>a</sub> prediction.
J. Cheminformatics, 2011
2009
Software news and updates electronegativity equalization method: Parameterization and validation for organic molecules using the Merz-Kollman-Singh charge distribution scheme.
J. Comput. Chem., 2009
2008
<i>In Silico</i> Mutagenesis and Docking Studies of <i>Pseudomonas aeruginosa</i> PA-IIL Lectin Predicting Binding Modes and Energies.
J. Chem. Inf. Model., 2008
2006
Optimized and parallelized implementation of the electronegativity equalization method and the atom-bond electronegativity equalization method.
J. Comput. Chem., 2006
BMC Bioinform., 2006
2003
Coordination number of zinc ions in the phosphotriesterase active site by molecular dynamics and quantum mechanics.
J. Comput. Chem., 2003
2000
Stability of Complexes of Aromatic Amides with Bromide Anion: Quantitative Structure-Property Relationships.
J. Chem. Inf. Comput. Sci., 2000
TRITON: in silico construction of protein mutants and prediction of their activities.
Bioinform., 2000
1999
J. Chem. Inf. Comput. Sci., 1999
1998
A Molecular Modeling Study of the Catalytic Mechanism of Haloalkane Dehalogenase. 2. Quantum Chemical Study of Complete Reaction Mechanism.
J. Chem. Inf. Comput. Sci., 1998
1997
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., 1997
1995
Conformational Analysis and Flexibility of Carbohydrates Using the CICADA Approach with MM3.
J. Comput. Chem., 1995
1994
J. Comput. Chem., 1994
1991
MAPOS: a computer program for organic synthesis design based on synthon model of organic chemistry.
J. Chem. Inf. Comput. Sci., 1991