Jaroslav Koča

发表

bio.tools Sum – tool for exploration of summary information about bioinformatics services in bio.tools

Tomáš Raček, Radka Svobodová Vařeková, Dan Polanský, 2018 .

Computational prediction of monosaccharide binding free energies to lectins with linear interaction energy models

Jaroslav Koča, Sushil Kumar Mishra, Johan Sund, 2012, J. Comput. Chem..

Biomacromolecular Fragments and Patterns

Radka Svobodová Vařeková, Karel Berka, Jaroslav Koča, 2016 .

Structural Bioinformatics Databases of General Use

Radka Svobodová Vařeková, Karel Berka, Jaroslav Koča, 2016 .

CCL - Charge Calculation Language

Tomáš Raček, Radka Svobodová Vařeková, Jaroslav Koča, 2018 .

NEEMP – Tool for parameterization of empirical chargecalculation method EEM

Radka Svobodová Vařeková, Jaroslav Koča, Tomáš Raček, 2014 .

Comparison of protein structural motifs – challenges and algorithms. Improved approach and case studies

Radka Svobodová Vařeková, Jaroslav Koča, Lukáš Pravda, 2011 .

PMFLib – A TOOLKIT FOR FREE ENERGY CALCULATIONS II

Jaroslav Koča, Petr Kulhánek, István Simon, 2011 .

Catch-All Virtual Organizations - Solution for Heterogeneous and Disperse Grid Users Communities

Daniel Kouřil, Jaroslav Koča, Luděk Matyska, 2010 .

Exploring Trends in Quality of Biomacromolecular Structure Data

Radka Svobodová Vařeková, Jaroslav Koča, Vladimír Horský, 2017 .

QSPR modeling – algorithms, challenges and IT solutions

Radka Svobodová Vařeková, Jaroslav Koča, Stanislav Geidl, 2011 .

Detection and Extraction of Fragments

Radka Svobodová Vařeková, Karel Berka, Jaroslav Koča, 2016 .

The Synthon Model and the Program PEGAS for Computer AssistedOrganic Synthesis.

Eva Hladká, Jaroslav Koča, Milan Kratochvíl, 1993 .

Distributed CICADA—a case study of a parallelization of computational chemistry software for the distributed computing environment

Jaroslav Koča, Luděk Matyska, 2008 .

SiteBinder – software tool for superimposing multiple structural motives

Radka Svobodová Vařeková, Jaroslav Koča, Lukáš Pravda, 2010 .

Implementation and Testing of Multiple Walkers Approach BasedFree Energy Calculations in the Grid Environment

Jaroslav Koča, Luděk Matyska, Petr Kulhánek, 2009 .

Real-Time Interactive Visualisation of Large Macromolecular Assemblies and Molecular Machines at Atomic Resolution

Karel Berka, Jaroslav Koča, Sameer Velankar, 2017 .

CICADA: Parallelization and Related Problems

Jaroslav Koča, Zdeněk Kříž, Aleš Kosina, 2005 .

Biomacromolecular structure quality – improvement or stagnation?

Radka Svobodová Vařeková, Jaroslav Koča, Vladimír Horský, 2017 .

Web server for the rapid calculation of empirical atomic charges with QM accuracy

Radka Svobodová Vařeková, Jaroslav Koča, Stanislav Geidl, 2014 .

LiteMol suite: interactive web-based visualization of large-scale macromolecular structure data

Radka Svobodová Vařeková, Karel Berka, Jaroslav Koča, 2017, Nature Methods.

Automated Family-Wide Annotation of Secondary Structure Elements.

Karel Berka, Jaroslav Koča, Jan Hutař, 2019, Methods in molecular biology.

MotiveQuery: Web application for fast detection of biomacromolecular fragments in the entire Protein Data Bank

Radka Svobodová Vařeková, Jaroslav Koča, Lukáš Pravda, 2015 .

A Computer Program for the Simulation of the NOE Effect in NMRSpectroscopy, and Its Implementation into the CICADAConformational Search Program

Jaroslav Koča, Zdeněk Kříž, Per H.J. Carlsen, 2003 .

Molecular modeling in hands of protein engineers - thelectin-saccharide interaction study

Jaroslav Koča, Zdeněk Kříž, Jan Adam, 2007 .

Trends in biomacromolecular structure quality

Radka Svobodová Vařeková, Jaroslav Koča, Vladimír Horský, 2017 .

Trends in quality and properties of biomacromolecular complexes

Radka Svobodová Vařeková, Jaroslav Koča, Vladimír Horský, 2017 .

MotiveValidator: software for validation of ligand and residuestructures in biomolecular complexes

Radka Svobodová Vařeková, Jaroslav Koča, Lukáš Pravda, 2014 .

Anatomy of enzymatic channels and algorithm for its detection

Radka Svobodová Vařeková, Karel Berka, Jaroslav Koča, 2014 .

grid-CICADA: Efficient Explorer of Conformational Space ofBiomolecular Systems

Jaroslav Koča, Luděk Matyska, Petr Kulhánek, 2010 .

Synthon Model and Program PEGAS for Computer Assisted OrganicSynthesis

Eva Hladká, Jaroslav Koča, Luděk Matyska, 1993 .

Structural Bioinformatics Tools for Drug Design

Radka Svobodová Vařeková, Karel Berka, Jaroslav Koča, 2016, SpringerBriefs in Biochemistry and Molecular Biology.

VADER: New Software for Exploring Interconversions on Potential Energy Surfaces

Jaroslav Koča, Martin Černohorský, Sofiane Kettou, 1999, J. Chem. Inf. Comput. Sci..

TRITON 4 : software for ligand-binding protein engineering

Jaroslav Koča, Zdeněk Kříž, Jan Adam, 2009 .

SiteBinder – an improved software superimposing multipleprotein structural motifs and its applications

Radka Svobodová Vařeková, Jaroslav Koča, Stanislav Geidl, 2011 .

bio.tools Sum

Tomáš Raček, Radka Svobodová Vařeková, Dan Polanský, 2017 .

Do trends in biomacromolecular structure quality inspire optimism

Radka Svobodová Vařeková, Jaroslav Koča, Sameer Velankar, 2017 .

ValTrendsDB: Viewing structure quality from macro and micro perspective

Radka Svobodová Vařeková, Jaroslav Koča, Vladimír Horský, 2018 .

Structural Bioinformatics Tools for Drug Design: Extraction ofBiologically Relevant Information from Structural Databases

Radka Svobodová Vařeková, Karel Berka, Jaroslav Koča, 2016 .

Implementation of Parallel Analyzes of Molecular DynamicsSimulation Trajectories

Jaroslav Koča, Petr Kulhánek, Navnit Kumar Mishra, 2009 .

A metric for graphs

Jaroslav Koča, Vladimír Baláž, Vladimír Kvasnička, 1986 .

MotiveQuery: Language and Web Service for Fast Identification of Protein Structural Motifs in the Entire Protein Data Bank

Radka Svobodová Vařeková, Jaroslav Koča, Lukáš Pravda, 2014 .

Large-Scale Free Energy Calculations as Showcase of WorldwideGrid Usability

Jaroslav Koča, Luděk Matyska, Petr Kulhánek, 2009 .

Effective on-Demand Mining of Structural Databases

Jaroslav Koča, Lukáš Pravda, David Sehnal, 2017 .

Optimized SQE atomic charges for peptides accessible via a web application

Tomáš Raček, Karel Berka, Jaroslav Koča, 2021, Journal of Cheminformatics.

Correction to: Optimized SQE atomic charges for peptides accessible via a web application

Tomáš Raček, Karel Berka, Jaroslav Koča, 2021, Journal of Cheminformatics.

Importance of oligomerisation on Pseudomonas aeruginosaLectin-II binding affinity. In silico and in vitro mutagenesis

Jaroslav Koča, Michaela Wimmerová, Martina Pokorná, 2009, Journal of molecular modeling.

A mathematical model of the synthon

Jaroslav Koča, 1988 .

Ion Binding to Quadruplex DNA Stems. Comparison of MM and QM Descriptions Reveals Sizable Polarization Effects Not Included in Contemporary Simulations.

Jaroslav Koča, Holger Kruse, Arnošt Mládek, 2014, Journal of chemical theory and computation.

MOLE 2.0: Improved Approach for Analysis of Biomacromolecular Channels and Pores

Radka Svobodová Vařeková, Karel Berka, Jaroslav Koča, 2013 .

POTENTIAL ENERGY HYPERSURFACES OF NUCLEOTIDE SUGARS : AB INITIO CALCULATIONS, FORCE-FIELD PARAMETRIZATION, AND EXPLORATION OF THE FLEXIBILITY

Jaroslav Koča, Anne Imberty, Pavla Petrová, 1999 .

A mathematical model of realistic constitutional chemistry. A synthon approach. II: The model and organic synthesis

Jaroslav Koča, 1989 .

Computer program CICADA — travelling along conformational potential energy hypersurface

Jaroslav Koča, J. Koča, 1994 .

Regulatory Phosphorylations of Cyclin-Dependent Kinase 2: AnInsight from the Molecular Dynamics Simulations

Jaroslav Koča, Michal Otyepka, Iveta Bártová, 2008 .

Molecular dynamic simulations of protein/RNA complexes: CRISPR/Csy4 endoribonuclease.

Jaroslav Koča, Michal Otyepka, Carolina Estarellas, 2015, Biochimica et biophysica acta.

The Synthon Model and Organic Synthesis

Jaroslav Koča, L. Matyska, Vladimír Kvasnička, 1989 .

Influence of the Acetylcholinesterase Active Site Protonation on Omega Loop and Active Site Dynamics

Jaroslav Koča, Daniel Jun, Zdeněk Kříž, 2010, Journal of biomolecular structure & dynamics.

Comparison of force-fields parametrizations as applied to conformational analysis of ribofuranosides

Jaroslav Koča, Serge Pérez, Anne Imberty, 1998 .

Potential energy hypersurface and molecular flexibility

Jaroslav Koča, J. Koča, 1993 .

Conformations of Flanking Bases in HIV-1 RNA DIS Kissing Complexes Studied by Molecular Dynamics

Jaroslav Koča, Petr Kulhánek, Tadeusz Kulinski, 2007, Biophysical journal.

Regulatory phosphorylation of cyclin-dependent kinase 2: insights from molecular dynamics simulations

Jaroslav Koča, Michal Otyepka, J. Koča, 2008, Journal of molecular modeling.

A graph model of the synthon

Jaroslav Koča, 1988 .

Automated Training of ReaxFF Reactive Force Fields for Energetics of Enzymatic Reactions.

Jaroslav Koča, J. Koča, T. Trnka, 2018, Journal of chemical theory and computation.

Evaluation of Selected Classical Force Fields for Alchemical Binding Free Energy Calculations of Protein-Carbohydrate Complexes.

Jaroslav Koča, Hannes H. Loeffler, Julien Michel, 2015, Journal of chemical theory and computation.

Exploring reaction pathways for O-GlcNAc transferase catalysis. A string method study.

Jaroslav Koča, Petr Kulhánek, Stanislav Kozmon, 2015, The journal of physical chemistry. B.

Computer simulation of histo-blood group oligosaccharides: energy maps of all constituting disaccharides and potential energy surfaces of 14 ABH and Lewis carbohydrate antigens

Jaroslav Koča, Emmanuel Mikros, Serge Pérez, 1995, Glycoconjugate Journal.

Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations

Jaroslav Koča, Thomas E. Cheatham, Jiří Šponer, 2013, Nucleic acids research.

PDBe-KB: a community-driven resource for structural and functional annotations

Alfonso Valencia, Karel Berka, Jaroslav Koča, 2019, Nucleic Acids Res..

Stacking Interactions between Carbohydrate and Protein Quantified by Combination of Theoretical and Experimental Methods

Jaroslav Koča, Sushil Kumar Mishra, Jan Komárek, 2012, PloS one.

SINGLE-COORDINATE-DRIVING METHOD COUPLED WITH SIMULATED ANNEALING. AN EFFICIENT TOOL TO SEARCH CONFORMATIONAL SPACE

Jaroslav Koča, J. Koča, E. Fadrná, 1997 .

Synthon Model of Organic Chemistry and Synthesis Design

Jaroslav Koča, L. Matyska, Jiri Pospichal, 1989 .

A mathematical model of realistic constitutional chemistry. A synthon approach. I: An algebraic model of a synthon

Jaroslav Koča, J. Koča, 1989 .

A combination of driving method with simulated annealing to search conformational space

Jaroslav Koča, J. Koča, E. Fadrná, 1997 .

A mathematical model of the logical structure of chemistry. A bridge between theoretical and experimental chemistry and a general tool for computer-assisted molecular design

Jaroslav Koča, J. Koča, 1991 .

How Mycobacterium tuberculosis Galactofuranosyl Transferase 2 (GlfT2) Generates Alternating β-(1-6) and β-(1-5) Linkages: A QM/MM Molecular Dynamics Study of the Chemical Steps.

Jaroslav Koča, Stanislav Kozmon, J. Koča, 2018, Chemistry.

Assessing the Performance of MM/PBSA, MM/GBSA, and QM-MM/GBSA Approaches on Protein/Carbohydrate Complexes: Effect of Implicit Solvent Models, QM Methods, and Entropic Contributions.

Jaroslav Koča, J. Koča, S. Mishra, 2018, The journal of physical chemistry. B.