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D-Index & Metrics

Chemistry

D-Index
58
Citations
12733
World Ranking
10566
National Ranking
47

Overview

Jaroslav Koča was affiliated with the Central European Institute of Technology in the Czech Republic. Their research primarily focused on the field of Biochemistry, Genetics, and Molecular Biology, producing 28 publications within this domain. Within this main field, their work spanned several subfields, including Molecular Biology, Materials Chemistry, Pharmacology, Radiology, Nuclear Medicine and Imaging, and Physical and Theoretical Chemistry.

The scientist's main research topics included Protein Structure and Dynamics, Enzyme Structure and Function, Glycosylation and Glycoproteins Research, Monoclonal and Polyclonal Antibodies Research, Computational Drug Discovery Methods, Genomics and Phylogenetic Studies, and Pharmacogenetics and Drug Metabolism.

Koča collaborated frequently with several researchers, including Radka Svobodová Vařeková, Karel Berka, David Sehnal, Adam Midlik, and Veronika Navrátilová. These partnerships contributed to a substantial body of work within their scientific community.

Their publications appeared most often in venues such as Zenodo (CERN European Organization for Nuclear Research), Nucleic Acids Research, Journal of Cheminformatics, ACS Omega, and Acta Crystallographica Section D Structural Biology. Zenodo hosted three of their works, while they published two articles each in Nucleic Acids Research, Journal of Cheminformatics, ACS Omega, and Acta Crystallographica Section D Structural Biology.

Notable recent papers included:

  • Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures, 2021, Nucleic Acids Research
  • Selectins-The Two Dr. Jekyll and Mr. Hyde Faces of Adhesion Molecules-A Review, 2020, Molecules
  • The CH-π Interaction in Protein-Carbohydrate Binding: Bioinformatics and In Vitro Quantification, 2020, Chemistry - A European Journal
  • Atomic Charge Calculator II: web-based tool for the calculation of partial atomic charges, 2020, Nucleic Acids Research
  • BinaryCIF and CIFTools-Lightweight, efficient and extensible macromolecular data management, 2020, PLoS Computational Biology

These works contributed to the understanding and analysis of biomolecular structures, adhesion molecules, protein-carbohydrate interactions, atomic charge calculations, and macromolecular data management, reflecting a broad expertise within molecular biosciences.

Best Publications

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

    Stephen K Burley;Helen M Berman;Charmi Bhikadiya

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

    David Sehnal;David Sehnal;David Sehnal;Sebastian Bittrich;Mandar S Deshpande;Radka Svobodová;Radka Svobodová

  • Structures and mechanisms of glycosyltransferases

    Christelle Breton;Lenka Šnajdrová;Charlotte Jeanneau;Jaroslav Koča

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

    Martin Petřek;Michal Otyepka;Pavel Banáš;Pavlína Košinová

  • MOLE 2.0: advanced approach for analysis of biomacromolecular channels

    David Sehnal;David Sehnal;Radka Svobodová Vařeková;Karel Berka;Lukáš Pravda

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

    Pravda L;Sehnal D;Sehnal D;Toušek D;Navrátilová

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

    Martin Petřek;Pavlína Košinová;Jaroslav Koča;Michal Otyepka

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

    Miroslav Krepl;Marie Zgarbová;Petr Stadlbauer;Michal Otyepka

  • PDBe: improved findability of macromolecular structure data in the PDB.

    David R Armstrong;John M Berrisford;Matthew J Conroy;Aleksandras Gutmanas

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

    Eva Fadrná;Nad’a Špačková;Joanna Sarzyñska;Jaroslav Koča

  • Acetylcholinesterases – the structural similarities and differences

    Jiří Wiesner;Zdeněk Kříž;Kamil Kuča;Daniel Jun

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

    Eva Fadrná;Naděžda Špačková;Richard Štefl;Richard Štefl;Jaroslav Koča

  • Non-Watson-Crick Basepairing and Hydration in RNA Motifs: Molecular Dynamics of 5S rRNA Loop E

    Kamila Réblová;Nad’a Špačková;Richard Štefl;Kristina Csaszar

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

    David Sehnal;Alexander S. Rose;Jaroslav Koca;Stephen K. Burley

  • MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels

    Karel Berka;Ondřej Hanák;David Sehnal;Pavel Banáš

  • 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

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

    Petr Stadlbauer;Miroslav Krepl;Thomas E. Cheatham;Jaroslav Koča

  • Formation Pathways of a Guanine-Quadruplex DNA Revealed by Molecular Dynamics and Thermodynamic Analysis of the Substates

    Richard Štefl;Thomas E. Cheatham;Naděžda Špačková;Eva Fadrná

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

    David Sehnal;Mandar Deshpande;Radka Svobodová Vařeková;Radka Svobodová Vařeková;Saqib Mir

  • An A-type Double Helix of DNA Having B-type Puckering of the Deoxyribose Rings

    Lukáš Trantı́rek;Richard Štefl;Michaela Vorlı́čková;Jaroslav Koča

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

    Mihaly Varadi;John Berrisford;Mandar Deshpande;Sreenath S. Nair

Frequent Co-Authors

Michal Otyepka
Michal Otyepka Palacký University, Olomouc
Jiří Šponer
Jiří Šponer Masaryk University
Anne Imberty
Anne Imberty Grenoble Alpes University
Sameer Velankar
Sameer Velankar European Bioinformatics Institute
Neocles B. Leontis
Neocles B. Leontis Bowling Green State University
Serge Pérez
Serge Pérez Centre national de la recherche scientifique, CNRS
Pavel Banáš
Pavel Banáš Palacký University, Olomouc
Stephen K. Burley
Stephen K. Burley Rutgers, The State University of New Jersey
Thomas E. Cheatham
Thomas E. Cheatham University of Utah
Ruben Abagyan
Ruben Abagyan University of California, San Diego

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