J. Koča

发表

The Molecular Graphs

L. Matyska, J. Koča, M. Kratochvíl, 1989 .

Long-residency hydration, cation binding, and dynamics of loop E/helix IV rRNA-L25 protein complex.

K. Réblová, J. Šponer, N. Leontis, 2004, Biophysical journal.

TRITON: graphic software for rational engineering of enzymes.

J. Koča, J. Damborský, J. Damboský, 2001, Trends in biochemical sciences.

NEEMP: software for validation, accurate calculation and fast parameterization of EEM charges

Radka Svobodová Vareková, Jaroslav Koca, Ales Krenek, 2016, Journal of Cheminformatics.

Electronegativity Equalization Method: Parameterization and Validation for Large Sets of Organic, Organohalogene and Organometal Molecule

Simon Suchomel, J. Koča, R. Vareková, 2007, International Journal of Molecular Sciences.

Mobility of the active site bound paraoxon and sarin in zinc-phosphotriesterase by molecular dynamics simulation and quantum chemical calculation.

R. Ornstein, J. Koča, C. Zhan, 2001, Journal of the American Chemical Society.

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

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

Long-range Electrostatic Interactions in Molecular Dynamics: An Endothelin-1 Case Study

Jaroslav Koca, J. Koča, E. Fadrná, 2005, Journal of biomolecular structure & dynamics.

In Silico Engineering of Proteins That Recognize Small Molecules

J. Koča, S. Mishra, G. Demo, 2012 .

Charge-perturbation dynamics — a new avenue towards in silico protein folding

J. Koča, P. Pant, Ravi José Tristão Ramos, 2019, bioRxiv.

Reference simulations of noncanonical nucleic acids with different χ variants of the AMBER force field: quadruplex DNA, quadruplex RNA and Z-DNA.

J. Šponer, T. Cheatham, J. Koča, 2012, Journal of chemical theory and computation.

The synthon model and the program PEGAS for computer assisted organic synthesis

L. Matyska, J. Koča, M. Kratochvíl, 1993 .

Influence of the O-phosphorylation of serine, threonine and tyrosine in proteins on the amidic 15N chemical shielding anisotropy tensors

J. Koča, R. Boelens, V. Sklenar, 2013, Journal of biomolecular NMR.

Analysis of the reaction mechanism and substrate specificity of haloalkane dehalogenases by sequential and structural comparisons.

J. Koča, J. Damborský, 1999, Protein engineering.

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

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

Functional flexibility of human cyclin‐dependent kinase‐2 and its evolutionary conservation

Jaroslav Koca, Michal Otyepka, J. Koča, 2007, Protein science : a publication of the Protein Society.

Structure, dynamics, and elasticity of free 16s rRNA helix 44 studied by molecular dynamics simulations

Jaroslav Koca, Filip Rázga, Filip Lankas, 2006, Biopolymers.

Travelling through conformational space: an approach for analyzing the conformational behaviour of flexible molecules.

J. Koča, J Koca, 1998, Progress in biophysics and molecular biology.

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

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

Travelling on the potential energy surfaces of carbohydrates: comparative application of an exhaustive systematic conformational search with an heuristic search.

S. Engelsen, J. Koča, C. Hervé du Penhoat, 1995, Carbohydrate research.

Catalytic Mechanism of Processive GlfT2: Transition Path Sampling Investigation of Substrate Translocation

C. Dellago, J. Koča, P. Janoš, 2020, ACS omega.

Detection of Channels

Radka Svobodová Vareková, J. Koča, K. Berka, 2016 .

REVIEW Structures and mechanisms of glycosyltransferases

A. Imberty, J. Koča, C. Breton, 2006 .

Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations

J. Šponer, J. Koča, G. Bussi, 2015, Nucleic acids research.

Triplex intermediates in folding of human telomeric quadruplexes probed by microsecond-scale molecular dynamics simulations.

J. Šponer, T. Cheatham, J. Koča, 2014, Biochimie.

The Eighth Central European Conference “Chemistry towards Biology”: Snapshot

J. Koča, S. Geidl, V. Horský, 2016, Molecules.

PDBe: improved findability of macromolecular structure data in the PDB

Radka Svobodová Vareková, Alice R. Clark, A. R. Clark, 2019, Nucleic Acids Res..

Three-dimensional homology model of GlcNAc-TV glycosyltransferase.

J. Koča, P. Janoš, I. Tvaroška, 2016, Glycobiology.

Conformational features of linear and cyclic enkephalins. A computational study

J. Koča, P. Carlsen, Z. Kríz, 2001 .

CICADA interface with AMBER. An application on oligonucleotides and their fragments.

J. Koča, E. Fadrná, 1996, Journal of biomolecular structure & dynamics.

Single-coordinate-driving method for molecular docking: application to modeling of guest inclusion in cyclodextrin.

J. Koča, S. Pérez, A. Imberty, 2000, Journal of molecular graphics & modelling.

Cyclin-Dependent Protein Kinase-2 Regulation byPhosphorylation, A Molecular Dynamics Study

J. Koča, M. Otyepka, Z. Kríz, 2003 .

High-quality and universal empirical atomic charges for chemoinformatics applications

Radka Svobodová Vareková, Jaroslav Koca, Ruben Abagyan, 2015, Journal of Cheminformatics.

Atomic Charge Calculator II: web-based tool for the calculation of partial atomic charges

J. Koča, K. Berka, R. Vareková, 2020, Nucleic Acids Res..

Characterization via Charges

J. Koča, K. Berka, R. Vareková, 2016 .

Mol*: Towards a Common Library and Tools for Web Molecular Graphics

Sameer Velankar, David Sehnal, Stephen K. Burley, 2018, MolVa@EuroVis.

Influence of Trp flipping on carbohydrate binding in lectins. An example on Aleuria aurantia lectin AAL

J. Koča, P. Romano, S. Mishra, 2017, PloS one.

Uncovering of cytochrome P450 anatomy by SecStrAnnotator

J. Koča, K. Berka, T. Moturu, 2020, Scientific Reports.

Quantum-Chemical Insight Into Mechanism of Combined Intra-Intermolecular Cycloaddition

P. Kulhánek, J. Koča, M. Potáček, 2004 .

ROSE, a computer program for automatic generation of probable conformations

J. Koča, P. Carlsen, 1992 .

Effect of Cation Concentration on Molecular Dynamics Simulations of UDP-Glucose

A. Imberty, J. Koča, P. Petrová, 2000 .

Behavior of BsoBI endonuclease in the presence and absence of DNA

P. Kulhánek, J. Koča, Ivo Kabelka, 2017, Journal of Molecular Modeling.

Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA

J. Šponer, J. Koča, A. Mokdad, 2007, Nucleic acids research.

Protein engineering study of β-mannosidase to set up a potential chemically efficient biocatalyst.

J. Koča, V. Křen, G. Demo, 2014, Glycobiology.

Interactions of Amyloid β Peptide 1–40 and Cerebrosterol

J. Koča, D. Řípová, Z. Kríz, 2012, Neurochemical Research.

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

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

NAChRDB: A Web Resource of Structure–Function Annotations to Unravel the Allostery of Nicotinic Acetylcholine Receptors

J. Koča, P. Pant, Ravi José Tristão Ramos, 2021, ACS omega.

High affinity fucose binding of Pseudomonas aeruginosa lectin PA‐IIL: 1.0 Å resolution crystal structure of the complex combined with thermodynamics and computational chemistry approaches

Jaroslav Koca, Michaela Wimmerová, Martina Pokorná, 2004, Proteins: Structure, Function, and Bioinformatics.

Selectins—The Two Dr. Jekyll and Mr. Hyde Faces of Adhesion Molecules—A Review

J. Koča, C. Selvaraj, I. Tvaroška, 2020, Molecules.

From the Amide Bond Activation to Simultaneous Recognition of Anion-Cation Couple

J. Koča, I. Stibor, J. Hodačová, 1998 .

Computational Studies on the Stability of [Amide]Br- Complexes

J. Koča, I. Stibor, M. Čajan, 1999 .

The conformational behaviour of thiacalix[4]arenes: the pinched cone–pinched cone transition

J. Koča, I. Stibor, H. Dvořáková, 2002 .

Investigation of the complexation of (+)-catechin by beta-cyclodextrin by a combination of NMR, microcalorimetry and molecular modeling techniques.

A. Imberty, J. Koča, R. Auzély-Velty, 2003, Organic & biomolecular chemistry.

Stability of Complexes of Aromatic Amides with Bromide Anion: Quantitative Structure-Property Relationships

Jaroslav Koca, Jirí Damborský, Michal Cajan, 2000, J. Chem. Inf. Comput. Sci..

The CH-π interaction in protein - carbohydrate binding: Bioinformatics and in vitro quantification.

J. Koča, M. Wimmerová, J. Houser, 2020, Chemistry.

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

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

Dispersion interactions of carbohydrates with condensate aromatic moieties: theoretical study on the CH-π interaction additive properties.

J. Koča, V. Spiwok, S. Kozmon, 2011, Physical chemistry chemical physics : PCCP.

Three-dimensional potential energy surface of selected carbohydrates' CH/π dispersion interactions calculated by high-level quantum mechanical methods.

J. Koča, V. Spiwok, S. Kozmon, 2011, Chemistry.

The structure and dynamics of chitin nanofibrils in an aqueous environment revealed by molecular dynamics simulations

Zora Strelcová, P. Kulhánek, J. Koča, 2016 .

Structures and mechanisms of glycosyltransferases.

Jaroslav Koca, Anne Imberty, Charlotte Jeanneau, 2006, Glycobiology.

Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields.

J. Šponer, M. Orozco, T. Kulinski, 2009, Journal of chemical theory and computation.

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

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

Molecular dynamics simulations of RNA kissing-loop motifs reveal structural dynamics and formation of cation-binding pockets.

Jaroslav Koca, K. Réblová, J. Šponer, 2003, Nucleic acids research.

Non-Watson-Crick basepairing and hydration in RNA motifs: molecular dynamics of 5S rRNA loop E.

Jaroslav Koca, Neocles B Leontis, K. Réblová, 2003, Biophysical journal.

Extended molecular dynamics of a c-kit promoter quadruplex

Stephen Neidle, Jaroslav Koca, Shozeb Haider, 2015, Nucleic acids research.

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.

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.

Molecular dynamics simulations of Guanine quadruplex loops: advances and force field limitations.

Jaroslav Koca, Thomas E Cheatham, J. Šponer, 2004, Biophysical journal.

Bioinformatics and molecular dynamics simulation study of L1 stalk non-canonical rRNA elements: kink-turns, loops, and tetraloops.

K. Réblová, J. Šponer, J. Koča, 2013, The journal of physical chemistry. B.

MOLE: a Voronoi diagram-based explorer of molecular channels, pores, and tunnels.

Jaroslav Koca, Michal Otyepka, Martin Petrek, 2007, Structure.

A conformational study of the xyloglucan oligomer, XXXG, by NMR spectroscopy and molecular modeling.

A. Imberty, J. Koča, C. Hervé du Penhoat, 2000, Biopolymers.

Protein Data Bank: the single global archive for 3D macromolecular structure data

Cole H. Christie, Jose M. Duarte, Rachel Kramer Green, 2018, Nucleic acids research.

MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels

Karel Berka, Radka Svobodová Vareková, Jaroslav Koca, 2012, Nucleic Acids Res..

How Ionic Strength Affects the Conformational Behavior of Human and Rat Beta Amyloids – A Computational Study

J. Koča, Z. Kríz, Z. Krištofíková, 2013, PloS one.

Substrate-assisted catalytic mechanism of O-GlcNAc transferase discovered by quantum mechanics/molecular mechanics investigation.

J. Koča, M. Wimmerová, I. Tvaroška, 2012, Journal of the American Chemical Society.

A QM/MM investigation of the catalytic mechanism of metal-ion-independent core 2 β1,6-N-acetylglucosaminyltransferase.

J. Koča, M. Wimmerová, I. Tvaroška, 2013, Chemistry.

Enhanced conformational sampling of carbohydrates by Hamiltonian replica-exchange simulation.

Sushil Kumar Mishra, Jaroslav Koca, Martin Zacharias, 2014, Glycobiology.

Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures

Radka Svobodová Vareková, Alexander S. Rose, S. Burley, 2021, Nucleic Acids Res..

Molecular dynamics simulations of solvated UDP-glucose in interaction with Mg2+ cations.

A. Imberty, J. Koča, P. Petrová, 2001, European journal of biochemistry.

Docking-based development of purine-like inhibitors of cyclin-dependent kinase-2.

J. Koča, M. Otyepka, M. Strnad, 2000, Journal of medicinal chemistry.

Different QM/MM Approaches To Elucidate Enzymatic Reactions: Case Study on ppGalNAcT2.

J. Koča, T. Trnka, P. Janoš, 2016, Journal of chemical theory and computation.

CAVER: a new tool to explore routes from protein clefts, pockets and cavities

Jaroslav Koca, Michal Otyepka, Jirí Damborský, 2006, BMC Bioinformatics.

Conformational behavior of nucleotide-sugar in solution: molecular dynamics and NMR study of solvated uridine diphosphate-glucose in the presence of monovalent cations.

A. Imberty, J. Koča, C. Hervé du Penhoat, 2001, Biopolymers.

MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update)

Karel Berka, Radka Svobodová Vareková, Jaroslav Koca, 2018, Nucleic Acids Res..

BinaryCIF and CIFTools—Lightweight, efficient and extensible macromolecular data management

Sameer Velankar, David Sehnal, Alexander S. Rose, 2020, PLoS Comput. Biol..

Synthon Model of Organic Chemistry and Synthesis Design

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

Molecular dynamics of DNA quadruplex molecules containing inosine, 6-thioguanine and 6-thiopurine.

J. Šponer, R. Stefl, J. Koča, 2001, Biophysical journal.

MOLE 2.0: advanced approach for analysis of biomacromolecular channels

Karel Berka, Radka Svobodová Vareková, Jaroslav Koca, 2013, Journal of Cheminformatics.

An A-type double helix of DNA having B-type puckering of the deoxyribose rings.

R. Stefl, J. Koča, V. Sklenar, 2000, Journal of molecular biology.

Enantioselective chromatography and molecular modeling of novel aryloxyaminopropan-2-ols with the alkyl carbamate function.

J. Koča, Z. Kríz, R. Opatrilova, 2004, Chirality.

Biomacromolecular Fragments and Patterns

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

Detection and Extraction of Fragments

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

PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank

Radka Svobodová Vareková, Jaroslav Koca, David Sehnal, 2015, Nucleic Acids Res..

SiteBinder: An Improved Approach for Comparing Multiple Protein Structural Motifs

Radka Svobodová Vareková, Jaroslav Koca, Stanislav Geidl, 2012, J. Chem. Inf. Model..

Structure , Dynamics , and Elasticity of Free 16 S rRNA Helix 44 Studied by Molecular Dynamics Simulations

Filip Rázga, K. Réblová, J. Šponer, 2006 .

VALIDATION OF TWO CONFORMATIONAL SEARCHING METHODS APPLIED TO SUCROSE : SIMULATION OF NMR AND CHIRO-OPTICAL DATA

A. Imberty, J. Koča, S. Pérez, 1997 .

A novel mechanism of proton transfer in protonated peptides.

Jaroslav Koca, Petr Kulhánek, P. Kulhánek, 2003, Journal of the American Chemical Society.

The reaction distance

J. Koča, 1988 .

Different Mechanisms of CDK5 and CDK2 Activation as Revealed by CDK5/p25 and CDK2/Cyclin A Dynamics*

J. Koča, M. Otyepka, Z. Kríz, 2006, Journal of Biological Chemistry.

The mechanism of inhibition of the cyclin‐dependent kinase‐2 as revealed by the molecular dynamics study on the complex CDK2 with the peptide substrate HHASPRK

Jaroslav Koca, Michal Otyepka, Zdenek Kríz, 2005, Protein science : a publication of the Protein Society.

Activation and inhibition of cyclin‐dependent kinase‐2 by phosphorylation; a molecular dynamics study reveals the functional importance of the glycine‐rich loop

Jaroslav Koca, Michal Otyepka, Zdenek Kríz, 2004, Protein science : a publication of the Protein Society.

The evolutionary advantage of toxin production among cyanobacteria, the oldest known organisms on Earth

J. Koča, Ravi José Tristão Ramos, Crina-Maria Ionescu, 2019, bioRxiv.

DAISY, a computational method: a novel tool for the study of the conformational behavior of flexible molecules

J. Koča, P. Carlsen, 1992 .

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

J. Koča, 1991 .

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

Jaroslav Koča, J. Koča, 1989 .

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.

Stepwise Catalytic Mechanism via Short-Lived Intermediate Inferred from Combined QM/MM MERP and PES Calculations on Retaining Glycosyltransferase ppGalNAcT2

Jaroslav Koca, Tomás Trnka, Stanislav Kozmon, 2014, PLoS Comput. Biol..

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.

Acetylcholinesterases – the structural similarities and differences

Jaroslav Koca, Kamil Kuca, Daniel Jun, 2007, Journal of enzyme inhibition and medicinal chemistry.

Repositioning the catalytic triad aspartic acid of haloalkane dehalogenase: effects on stability, kinetics, and structure.

J. Koča, J. Damborský, G. H. Krooshof, 1997, Biochemistry.

Conformational behavior and flexibility of terminally blocked alanine di- and tripeptides

J. Koča, P. Carlsen, 1993 .

Conformational Flexibility of Two RNA Trimers Explored by Computational Tools and Database Search

J. Koča, E. Fadrná, 2003, Journal of biomolecular structure & dynamics.

Predicting Non-Sentinel Lymph Node Status After Positive Sentinel Biopsy in Breast Cancer: What Model Performs the Best in a Czech Population?

J. Koča, T. Pavlík, P. Fabián, 2009, Pathology & Oncology Research.

ChannelsDB: database of biomacromolecular tunnels and pores

Karel Berka, Radka Svobodová Vareková, Jaroslav Koca, 2017, Nucleic Acids Res..

Anatomy of enzyme channels

Karel Berka, Radka Svobodová Vareková, Jaroslav Koca, 2014, BMC Bioinformatics.

Ribosomal RNA Kink-turn Motif—A Flexible Molecular Hinge

Jaroslav Koca, Filip Rázga, Neocles B Leontis, 2004, Journal of biomolecular structure & dynamics.

Why acetylcholinesterase reactivators do not work in butyrylcholinesterase

J. Koča, K. Kuča, D. Jun, 2010, Journal of enzyme inhibition and medicinal chemistry.

Predicting pKa values from EEM atomic charges

Radka Svobodová Vareková, Jaroslav Koca, Ruben Abagyan, 2013, Journal of Cheminformatics.

Predicting pKa Values of Substituted Phenols from Atomic Charges: Comparison of Different Quantum Mechanical Methods and Charge Distribution Schemes

Radka Svobodová Vareková, Jaroslav Koca, Ruben Abagyan, 2011, J. Chem. Inf. Model..

QSPR designer – a program to design and evaluate QSPR models. Case study on pKa prediction

Radka Svobodová Vareková, Jaroslav Koca, Stanislav Geidl, 2011, J. Cheminformatics.

Software news and updates electronegativity equalization method: Parameterization and validation for organic molecules using the Merz‐Kollman‐Singh charge distribution scheme

Radka Svobodová Vareková, Jaroslav Koca, Zuzana Jirousková, 2009, J. Comput. Chem..

Optimized and parallelized implementation of the electronegativity equalization method and the atom‐bond electronegativity equalization method

Radka Svobodová Vareková, Jaroslav Koca, J. Koča, 2006, J. Comput. Chem..

Molecular orbital calculations to describe microbial reductive dechlorination of polychlorinated dioxins

J. Koča, J. Damborský, P. Adriaens, 1998 .

MotiveValidator: interactive web-based validation of ligand and residue structure in biomolecular complexes

Radka Svobodová Vareková, Jaroslav Koca, Stanislav Geidl, 2014, Nucleic Acids Res..

TRITON: a graphical tool for ligand-binding protein engineering

Jaroslav Koca, Zdenek Kríz, Jan Adam, 2008, Bioinform..

Conformational analysis of complex oligosaccharides: the CICADA approach to the uromodulin O-glycans.

Jaroslav Koca, Serge Pérez, J. Koča, 2004, Carbohydrate research.

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.

Recognition of selected monosaccharides by Pseudomonas aeruginosa Lectin II analyzed by molecular dynamics and free energy calculations.

Jaroslav Koca, Zdenek Kríz, Michaela Wimmerová, 2010, Carbohydrate research.

AtomicChargeCalculator: interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules

Radka Svobodová Vareková, Jaroslav Koca, Stanislav Geidl, 2015, Journal of Cheminformatics.

Engineering the Pseudomonas aeruginosa II lectin: designing mutants with changed affinity and specificity

Jaroslav Koca, Zdenek Kríz, Jan Adam, 2014, Journal of Computer-Aided Molecular Design.

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

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

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.

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.

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..

In Silico Mutagenesis and Docking Study of Ralstonia solanacearum RSL Lectin: Performance of Docking Software To Predict Saccharide Binding

Sushil Kumar Mishra, Jaroslav Koca, Jan Adam, 2012, J. Chem. Inf. Model..

In Silico Mutagenesis and Docking Studies of Pseudomonas aeruginosa PA-IIL Lectin Predicting Binding Modes and Energies

Jaroslav Koca, Zdenek Kríz, Jan Adam, 2008, J. Chem. Inf. Model..

Molecular dynamics simulations of glycosyltransferase LgtC.

P. Kulhánek, A. Imberty, J. Koča, 2004, Carbohydrate research.

Computer program CICADA — travelling along conformational potential energy hypersurface

Jaroslav Koča, J. Koča, 1994 .

The catalytic reaction mechanism of tyrosylprotein sulfotransferase-1.

J. Koča, I. Tvaroška, P. Šmak, 2021, Physical chemistry chemical physics : PCCP.

Formation pathways of a guanine-quadruplex DNA revealed by molecular dynamics and thermodynamic analysis of the substates.

Jaroslav Koca, Thomas E Cheatham, J. Šponer, 2003, Biophysical journal.

Halide-stabilizing residues of haloalkane dehalogenases studied by quantum mechanic calculations and site-directed mutagenesis.

Yuji Nagata, Jaroslav Koca, Jirí Damborský, 2002, Biochemistry.

A Molecular Modeling Study of the Catalytic Mechanism of Haloalkane Dehalogenase: 1. Quantum Chemical Study of the First Reaction Step

Jaroslav Koca, Jirí Damborský, Miroslav Nemec, 1997, J. Chem. Inf. Comput. Sci..

CONFORMATIONAL BEHAVIOR AND FLEXIBILITY OF MET-ENKEPHALIN

J. Koča, P. Carlsen, 1995 .

D‐CICADA: A software for conformational PES elucidation on network of workstations

Jaroslav Koca, Ludek Matyska, L. Matyska, 1994, J. Comput. Chem..

Computer study of conformational flexibility of 20 common amino acids

J. Koča, P. Carlsen, Z. Kříž, 1994 .

Conformational Behavior and Flexibility of Terminally Blocked Cysteine and Cystine

J. Koča, P. Carlsen, Z. Kříž, 1996 .

Computer simulation of conformational movement based on interconversion phenomena

J. Koča, 1995 .

Potential energy hypersurface and molecular flexibility

Jaroslav Koča, J. Koča, 1993 .

Complexity and Convergence of Electrostatic and van der Waals Energies within PME and Cutoff Methods

J. Koča, R. Vareková, C. Zhan, 2004 .

Analysis of CDK2 active‐site hydration: A method to design new inhibitors

J. Koča, M. Otyepka, Iveta Bártová, 2004, Proteins.

Influence of the O-phosphorylation of serine, threonine and tyrosine in proteins on the amidic 15N chemical shielding anisotropy tensors

J. Koča, R. Boelens, V. Sklenar, 2013, Journal of biomolecular NMR.

Computational site-directed mutagenesis of haloalkane dehalogenase in position 172.

J. Koča, M. Bohác, J. Damborský, 1998, Protein engineering.

Hinge-like motions in RNA kink-turns: the role of the second a-minor motif and nominally unpaired bases.

J. Šponer, N. Leontis, J. Koča, 2005, Biophysical journal.

The Synthon Model and Organic Synthesis

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

SINGLE-COORDINATE-DRIVING METHOD COUPLED WITH SIMULATED ANNEALING. AN EFFICIENT TOOL 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 .

RNA kink-turns as molecular elbows: hydration, cation binding, and large-scale dynamics.

Jaroslav Koca, Martin Zacharias, Filip Rázga, 2006, Structure.

Coordination number of zinc ions in the phosphotriesterase active site by molecular dynamics and quantum mechanics

Jaroslav Koca, Chang-Guo Zhan, Rick L. Ornstein, 2003, J. Comput. Chem..

A Molecular Modeling Study of the Catalytic Mechanism of Haloalkane Dehalogenase. 2. Quantum Chemical Study of Complete Reaction Mechanism

Jaroslav Koca, Jirí Damborský, Michal Kutý, 1998, J. Chem. Inf. Comput. Sci..

Molecular modeling of glycosyltransferases.

A. Imberty, J. Koča, C. Breton, 2006, Methods in molecular biology.

Mechanism of Proton Transfer in Short Protonated Oligopeptides. 1. N-Methylacetamide and N2-Acetyl-N1-methylglycinamide

P. Kulhánek, J. Koča, E. W. Schlag, 2003 .

Rapid Calculation of Accurate Atomic Charges for Proteins via the Electronegativity Equalization Method

Radka Svobodová Vareková, Jaroslav Koca, Stanislav Geidl, 2013, J. Chem. Inf. Model..

Influence of stereochemistry on proton transfer in protonated tripeptide models

P. Kulhánek, J. Koča, N. A. Soliman, 2012, Journal of Molecular Modeling.

NAChRDB: A Web Resource of Structure-Function Annotations to Unravel the Allostery of Nicotinic Acetylcholine Receptors

Crina-Maria Ionescu, Purbaj Pant, Jaroslav Koča, 2020, bioRxiv.

Visualization and Analysis of Protein Structures with LiteMol Suite.

Karel Berka, Lukáš Pravda, David Sehnal, 2020, Methods in molecular biology.

High-performance macromolecular data delivery and visualization for the web

Karel Berka, David Sehnal, Alexander S. Rose, 2020, Acta crystallographica. Section D, Structural biology.

A-like guanine-guanine stacking in the aqueous DNA duplex of d(GGGGCCCC).

R. Stefl, J. Koča, V. Sklenar, 2001, Journal of molecular biology.

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.

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

Jaroslav Koča, Serge Pérez, Anne Imberty, 1998 .

PMFLib – A TOOLKIT FOR FREE ENERGY CALCULATIONS II

Jaroslav Koča, Petr Kulhánek, István Simon, 2011 .

Conformational analysis and flexibility of carbohydrates using the CICADA approach with MM3

Jaroslav Koca, Serge Pérez, Anne Imberty, 1995, J. Comput. Chem..

Charge Profile Analysis Reveals That Activation of Pro-apoptotic Regulators Bax and Bak Relies on Charge Transfer Mediated Allosteric Regulation

Radka Svobodová Vareková, Jaroslav Koca, Crina-Maria Ionescu, 2012, PLoS Comput. Biol..

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.

Pan-selectin inhibitors as potential therapeutics for COVID-19 treatment: in silico screening study

J. Koča, I. Tvaroška, P. Šmak, 2021, Glycobiology.

How Does the Methodology of 3D Structure Preparation Influence the Quality of pKa Prediction?

Radka Svobodová Vareková, Jaroslav Koca, Ruben Abagyan, 2015, J. Chem. Inf. Model..

TRITON: in silico construction of protein mutants and prediction of their activities

Jaroslav Koca, Jirí Damborský, Martin Prokop, 2000, Bioinform..

CAVER: a new tool to explore routes from protein clefts, pockets and cavities

J. Koča, J. Damborský, M. Otyepka, 2006, BMC Bioinformatics.

Unrestrained Molecular Dynamics Simulations of [d(AT)5]2 Duplex in Aqueous Solution: Hydration and Binding of Sodium Ions in the Minor Groove

J. Koča, Andreas Stefl, 2000 .

Different Mechanisms of CDK 5 and CDK 2 Activation as Revealed by CDK 5 / p 25 and CDK 2 / Cyclin A Dynamics

J. Koča, M. Otyepka, Iveta Bártová, 2006 .

ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank

Radka Svobodová Vareková, Jaroslav Koca, Stanislav Geidl, 2014, Nucleic Acids Res..

VADER: New Software for Exploring Interconversions on Potential Energy Surfaces

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

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.

Molecular dynamics study of Pseudomonas aeruginosa lectin‐II complexed with monosaccharides

Navnit Kumar Mishra, P. Kulhánek, A. Imberty, 2008, Proteins.

Interactions of Amyloid β Peptide 1–40 and Cerebrosterol

J. Koča, D. Řípová, Z. Krištofíková, 2011, Neurochemical Research.

CAVER: a new tool to explore routes from protein clefts, pockets and cavities

J. Koča, J. Damborský, M. Otyepka, 2006, BMC Bioinformatics.

Comparison of conformational behavior of the short alanine peptides and their boron analogues

J. Koča, M. Cernohorský, M. Vaultier*, 1999 .

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

Jaroslav Koča, Luděk Matyska, Petr Kulhánek, 2009 .

QSPR designer – employ your own descriptors in the automated QSAR modeling process

Radka Svobodová Vareková, Jaroslav Koca, Stanislav Geidl, 2012, Journal of Cheminformatics.

Bioinformatics and molecular dynamics simulation study of L1 stalk non-canonical rRNA elements: kink-turns, loops, and tetraloops.

K. Réblová, J. Šponer, J. Koča, 2013, The journal of physical chemistry. B.