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1

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

Zuzana Jiroušková, Radka Svobodová Vařeková, Jakub Vaněk, Jaroslav Koča

Journal:

Journal of Computational Chemistry

Year:

2009

Language:

english

File:

PDF, 79 KB

english, 2009

2

Different QM/MM Approaches to Elucidate Enzymatic Reactions: Case study on the ppGalNAcT2 glycosyltransferase

Janoš, Pavel, Trnka, Tomáš, Kozmon, Stanislav, Tvaroska, Igor, Koča, Jaroslav

Journal:

Journal of Chemical Theory and Computation

Year:

2016

Language:

english

File:

PDF, 1.97 MB

english, 2016

3

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

Gkionis, Konstantinos, Kruse, Holger, Platts, James A., Mládek, Arnošt, Koča, Jaroslav, Šponer, Jiří

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 2.79 MB

english, 2014

4

[SpringerBriefs in Biochemistry and Molecular Biology] Structural Bioinformatics Tools for Drug Design ||

Koča, Jaroslav, Svobodová Vařeková, Radka, Pravda, Lukáš, Berka, Karel, Geidl, Stanislav, Sehnal, David, Otyepka, Michal

Year:

2016

Language:

english

File:

PDF, 6.72 MB

english, 2016

5

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

Sehnal, David, Deshpande, Mandar, Svobodova Varekova, Radka, Mir, Saquib, Berka, Karel, Midlik, Adam, Pravda, Lukas, Velankar, Sameer, Koca, Jaroslav

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 47 KB

english, 2017

6

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

Trnka, Tomáš, Tvaroska, Igor, Koca, Jaroslav

Journal:

Journal of Chemical Theory and Computation

Year:

2017

Language:

english

File:

PDF, 1.10 MB

english, 2017

7

Binding Free Energy Calculation of Protein-Carbohydrate Complexes: Learnings so Far

Mishra, Sushil K., Koča, Jaroslav, Yamaguchi, Yoshiki

Journal:

Biophysical Journal

Year:

2018

Language:

english

File:

PDF, 44 KB

english, 2018

8

Interactive 3D Macromolecular Structure Data Mining with MolQL and Litemol Suite

Sehnal, David, Deshpande, Mandar, Rose, Alexander, Pravda, Lukas, Midlik, Adam, Svobodová Vařeková, Radka, Mir, Saqib, Berka, Karel, Velankar, Sameer, Koca, Jaroslav

Journal:

Biophysical Journal

Year:

2018

Language:

english

File:

PDF, 44 KB

english, 2018

9

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

Celine Picard, Jan Gruza, Christiane Derouet, C. M. G. C. Renard, Karim Mazeau, Jaroslav Koca, Anne Imberty, C. Hervé du Penhoat

Journal:

Year:

2000

Language:

english

File:

PDF, 417 KB

english, 2000

10

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

Pavla Petrová, Céline Monteiro, Catherine Hervé du Penhoat, Jaroslav Koča, Anne Imberty

Journal:

Year:

2001

Language:

english

File:

PDF, 351 KB

english, 2001

11

Three-Dimensional Potential Energy Surface of Selected Carbohydrates’ CH/π Dispersion Interactions Calculated by High-Level Quantum Mechanical Methods

Dr. Stanislav Kozmon, Radek Matuška, Dr. Vojtěch Spiwok, Prof. Dr. Jaroslav Koča

Journal:

Chemistry - A European Journal

Year:

2011

Language:

english

File:

PDF, 642 KB

english, 2011

12

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

Hana Navrátilová, Radka Opatřilová, Zdeněk Kříž, Jaroslav Koča

Journal:

Year:

2004

Language:

english

File:

PDF, 442 KB

english, 2004

13

Molecular orbital calculations to describe microbial reductive dechlorination of polychlorinated dioxins

Mary M. Lynam, Michal Kuty, Jiri Damborsky, Jaroslav Koca, Peter Adriaens

Journal:

Environmental Toxicology and Chemistry

Year:

1998

Language:

english

File:

PDF, 144 KB

english, 1998

14

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

Journal:

Journal of Computational Chemistry

Year:

2003

Language:

english

File:

PDF, 264 KB

english, 2003

15

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

Luděk Matyska, Jaroslav Koča

Journal:

Journal of Computational Chemistry

Year:

1994

Language:

english

File:

PDF, 841 KB

english, 1994

16

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

Jaroslav Koča, Serge Pérez, Anne Imberty

Journal:

Journal of Computational Chemistry

Year:

1995

Language:

english

File:

PDF, 1.03 MB

english, 1995

17

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

Søren B. Engelsen, Jaroslav Koca, Isabelle Braccini, Catherine Hervédu Penhoat, Serge Pérez

Journal:

Carbohydrate Research

Year:

1995

Language:

english

File:

PDF, 1.52 MB

english, 1995

18

Conformational behavior of pheromones and analogues Part I. 3-methyl-2-buten-1-ol, 3,3,6-trimethyl-1, 5- heptadien-4-ol and 2-methyl-6-methylene-2,7-octadien-4- on

Jaroslav Koča, Per H.J. Carlsen

Journal:

Journal of Molecular Structure

Year:

1991

Language:

english

File:

PDF, 645 KB

english, 1991

19

Conformational behavior of insect pheromones and analogues. Part II

Jaroslav Koča, Per H.J. Carlsen

Journal:

Journal of Molecular Structure

Year:

1992

Language:

english

File:

PDF, 1021 KB

english, 1992

20

Potential energy hypersurface and molecular flexibility

Journal:

Journal of Molecular Structure

Year:

1993

Language:

english

File:

PDF, 1.07 MB

english, 1993

21

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

Gianluca Cioci, Alain Rivet, Jaroslav Koča, Serge Pérez

Journal:

Carbohydrate Research

Year:

2004

Language:

english

File:

PDF, 593 KB

english, 2004

22

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

Pavla Petrová, Jaroslav Koča, Anne Imberty

Journal:

Year:

2001

Language:

english

File:

PDF, 1.64 MB

english, 2001

23

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

Zdeněk Kříž, Michal Otyepka, Iveta Bártová, Jaroslav Koča

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 975 KB

english, 2004

24

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

Edward P. Mitchell, Charles Sabin, Lenka Šnajdrová, Martina Pokorná, Stéphanie Perret, Catherine Gautier, Ctirad Hofr, Nechama Gilboa-Garber, Jaroslav Koča, Michaela Wimmerová, Anne Imberty

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 384 KB

english, 2005

25

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

Navnit Kumar Mishra, Petr Kulhánek, Lenka Šnajdrová, Martin Petřek, Anne Imberty, Jaroslav Koča

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 994 KB

english, 2008

26

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

Anne Imberty, Emmanuel Mikros, Jaroslav Koca, Rosella Mollicone, Rafael Oriol, Serge Pérez

Journal:

Glycoconjugate Journal

Year:

1995

Language:

english

File:

PDF, 1.60 MB

english, 1995

27

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

Journal:

Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta)

Year:

1991

Language:

english

File:

PDF, 601 KB

english, 1991

28

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

Journal:

Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta)

Year:

1991

Language:

english

File:

PDF, 1.23 MB

english, 1991

29

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

Journal:

Journal of Mathematical Chemistry

Year:

1989

Language:

english

File:

PDF, 829 KB

english, 1989

30

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

Journal:

Journal of Mathematical Chemistry

Year:

1989

Language:

english

File:

PDF, 1.39 MB

english, 1989

31

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

Iveta Bártová, Jaroslav Koča, Michal Otyepka

Journal:

Journal of Molecular Modeling

Year:

2008

Language:

english

File:

PDF, 266 KB

english, 2008

32

Importance of oligomerisation onPseudomonas aeruginosaLectin-II binding affinity.In silicoandin vitromutagenesis

Michaela Wimmerová, Navnit Kumar Mishra, Martina Pokorná, Jaroslav Koča

Journal:

Journal of Molecular Modeling

Year:

2009

Language:

english

File:

PDF, 277 KB

english, 2009

33

Influence of stereochemistry on proton transfer in protonated tripeptide models

Namat Ali Soliman, Petr Kulhánek, Jaroslav Koča

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 311 KB

english, 2012

34

Conformational Behavior and Flexibility of Terminally Blocked Cysteine and Cystine

Zdenek Kríz, Jaroslav Koca, PerH.J. Carlsen

Journal:

Journal of Molecular Modeling

Year:

1996

Language:

english

File:

PDF, 750 KB

english, 1996

35

Interactions of Amyloid β Peptide 1–40 and Cerebrosterol

Zdena Krištofiková, Zdeněk Kříž, Daniela Řípová, Jaroslav Koča

Journal:

Neurochemical Research

Year:

2012

Language:

english

File:

PDF, 362 KB

english, 2012

36

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

Oldřich Coufal, Tomáš Pavlík, Pavel Fabian, Rita Bori, Gábor Boross, István Sejben, Róbert Maráz, Jaroslav Koča, Eva Krejčí, Iva Horáková, Vendula Foltinová, Pavlína Vrtělová, Vojtech Chrenko, Wolde E

Journal:

Pathology & Oncology Research

Year:

2009

Language:

english

File:

PDF, 351 KB

english, 2009

37

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

Jaroslav Koča, Per H.J. Carlsen

Journal:

Journal of Molecular Structure

Year:

1993

Language:

english

File:

PDF, 1.16 MB

english, 1993

38

Molecular dynamics simulations of glycosyltransferase LgtC

Lenka Šnajdrová, Petr Kulhánek, Anne Imberty, Jaroslav Koča

Journal:

Carbohydrate Research

Year:

2004

Language:

english

File:

PDF, 787 KB

english, 2004

39

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

Navnit Kumar Mishra, Zdeněk Kříž, Michaela Wimmerová, Jaroslav Koča

Journal:

Carbohydrate Research

Year:

2010

Language:

english

File:

PDF, 1.16 MB

english, 2010

40

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

Jaroslav Koča, Martin Ludin, Serge Pérez, Anne Imberty

Journal:

Journal of Molecular Graphics and Modelling

Year:

2000

Language:

english

File:

PDF, 612 KB

english, 2000

41

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

Iveta Bártová, Michal Otyepka, Zdeněk Kříž, Jaroslav Koča

Journal:

Protein Science

Year:

2004

Language:

english

File:

PDF, 383 KB

english, 2004

42

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

Iveta Bártová, Jaroslav Koča, Michal Otyepka

Journal:

Protein Science

Year:

2008

Language:

english

File:

PDF, 986 KB

english, 2008

43

ROSE, a computer program for automatic generation of probable conformations

Jaroslav Koča, Per H.J. Carlsen

Journal:

Journal of Molecular Structure: THEOCHEM

Year:

1992

Language:

english

File:

PDF, 698 KB

english, 1992

44

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

Jaroslav Koča, Per H.J. Carlsen

Journal:

Journal of Molecular Structure: THEOCHEM

Year:

1992

Language:

english

File:

PDF, 1.78 MB

english, 1992

45

Conformational behavior and flexibility of met-enkephalin

Jaroslav Koča, Per H.J. Carlsen

Journal:

Journal of Molecular Structure: THEOCHEM

Year:

1995

Language:

english

File:

PDF, 602 KB

english, 1995

46

Computer program CICADA — travelling along conformational potential energy hypersurface

Journal:

Journal of Molecular Structure: THEOCHEM

Year:

1994

Language:

english

File:

PDF, 878 KB

english, 1994

47

Computer study of conformational flexibility of 20 common amino acids

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

Journal:

Journal of Molecular Structure: THEOCHEM

Year:

1994

Language:

english

File:

PDF, 625 KB

english, 1994

48

Computer simulation of conformational movement based on interconversion phenomena

Journal:

Journal of Molecular Structure: THEOCHEM

Year:

1995

Language:

english

File:

PDF, 721 KB

english, 1995

49

RNA Kink-Turns as Molecular Elbows: Hydration, Cation Binding, and Large-Scale Dynamics

Filip Rázga, Martin Zacharias, Kamila Réblová, Jaroslav Koča, Jiří Šponer

Journal:

Year:

2006

Language:

english

File:

PDF, 475 KB

english, 2006

50

MOLE: A Voronoi Diagram-Based Explorer of Molecular Channels, Pores, and Tunnels

Martin Petřek, Pavlína Košinová, Jaroslav Koča, Michal Otyepka

Journal:

Year:

2007

Language:

english

File:

PDF, 759 KB

english, 2007