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Curriculum vitae

Person Identification
  • Prof. RNDr. Jaroslav Koca, DrSc.
Institution
  • CEITEC Masaryk University
    and National Centre for Biomolecular Research
    Faculty of Science, Masaryk University
Function, current position
  • Professor and Director
Education and academic qualifications
  • 1995: Full Professor, Masaryk University, Brno (Chemistry)
  • 1993: D. Sc. (DrSc.) - Masaryk University, Brno (Chemistry)
  • 1988: Associate Professor, Masaryk University, Brno (Chemistry)
  • 1983: Ph. D. (CSc.) - Komensky University, Bratislava, Slovakia, (Chemistry)
  • 1983: Assistent Professor, Masaryk University, Brno (Chemistry)
  • 1979: M.S. (RNDr.) - Purkyne; University, Brno (Mathematics and Chemistry)
Professional experience
  • 2016-: Central European Institute of Technology (CEITEC) – Scientific director
  • 2009-2015: CEITEC Masaryk university – director of the Institute
  • 2009-2013: CEITEC – Scientific director for Life Science
  • 2001-: National Centre for Biomolecular Research, Fac Sci, Masaryk University, director
  • 1996-2000: Laboratory of Biomolecular Structure and Dynamics, Fac Sci, Masaryk University, head
  • 1995-: Dept of Organic Chemistry, Fac Sci, Masaryk University, professor
  • 1994-1995: Section Chemistry, Fac Sci, Masaryk University, head
  • 1988-1995: Dept of Organic Chemistry, Fac Sci, Masaryk University, associate professor
  • 1984-1988: Dept of Organic Chemistry, Fac Sci, Masaryk University, assistant professor
  • 1983-1984: Dept of Mathematics, Fac Sci, Masaryk University, assistant professor
Teaching activities
  • Mathematics and Computers for Chemists, Education in Chemistry, Molecular Modeling and Computer Assisted Chemistry and Biochemistry.
Research activities
  • Mathematical and computer assisted chemistry and biochemistry, computer assisted molecular modeling of biologically interesting chemical species, information technology in chemistry, biochemistry, and environmental chemistry. Last years mainly structural bioinformatics, conformational search, molecular docking and molecular dynamics simulations on peptides, proteins, oligonucleotides, nucleotide sugars, and carbohydrates. Methods for analysis conformational potential energy surfaces and energy landscapes of chemical reactions using molecular mechanics and quantum chemistry techniques. Publications include 6 monographs, 1 textbook, over 160 journal full text papers cited more than 3000 times, H-index 37, several computer programs and program systems. More about publications through Researcher ID (E-4460-2012) or ORCID (0000-0002-2780-4901). For more information se also http://www.chemi.muni.cz/~jkoca/
Professional stays abroad
  • 2002,2003: CERMAV CNRS Grenoble, France - 5 months visiting professor (VP)
  • 1999-2000: Pacific Northwest National Laboratory, Richland, WA, USA - 1 year (VP)
  • 1998: Univ. Grenoble, France - 3 months VP
  • 1996: Univ. Athens, Greece - 2 months VP
  • 1993: Univ. Nantes, France - 4 months VP
  • 1993: Univ. of Tennessee, Knoxville, USA - 2 months visiting researcher (VR)
  • 1992: Univ. Trondheim, Norway - 1 month VR
  • 1991: Univ. Rennes, France - 1 month - teaching doctoral course
  • 1991: Univ. Trondheim, Norway - 3 months VP
  • 1988-1990: Univ. Trondheim, Norway - 2 years NTNF postdoctoral fellow
  • 1985: Institute of Cybernetics and Information Processes, Berlin, Germany - 1 month - research stay
Other academic activities, research projects, grants
  • In charge of study curricula in chemistry at Faculty of Science, Masaryk University (2000-2007)
  • Member of Scientific Boards: Masaryk University (MU) (1998-9, 2006-), Faculty of Science MU (1997-9, 2003-), Faculty of Informatics MU (1995-2015)
  • Member of Doctoral Study Boards: organic chemistry, physical chemistry, biochemistry, biophysics, biomolecular chemistry
  • State examination commissions on undergraduate or doctoral level-chairman: education in chemistry, biomolecular chemistry
  • Deputy of the Department of Organic Chemistry (1992 - 2002 )
  • Academic senate (1991-1994)
  • Selected grants and long term research plans:
  • 2005-2011: Proteins in metabolism and during living systems interactions with the environment (MSM0021622413). Ministry of Education of the Czech Republic, principal investigator
  • 2005-2009: Calixarene-based multivalent glyco-drugs: design, structure, biological (antitumor and antiviral) activity (IAA400200503). Grant agency of the Academy of science of the Czech Republic, co-investigator
  • 2004-2008: Structural biophysics of macromolecules (204/03/H016). Grant agency of the Czech Republic, co-investigator
  • 2000-2004: Biomolecular Centre (LN00A016) Ministry of Education, principal investigator
  • 2005-2011: Structure-function relationships of biomolecules and its role in metabolism (CEZ:J07/98:143100005). Ministry of Education of the Czech Republic, principal investigator
  • 1998-2003: HCI LAB - Laboratory of man-machine interactions (201/98/KO41), GACR, co-investigator
  • 2000-2002: Amidic ligands: design synthesis and complexes with anion (203/00/1011), GACR, co-investigator
  • 1996-2000: Laboratory of Biomolecular Structure and Dynamics (VS96095), Ministry of Education, principal investigator
Non-university activities
  • Presidium of Czech Science Foundation (2016- )
  • ELIXIR CZ – Head of Board (2014- )
  • ELIXIR Board Europe – representative of the Czech Republic (2014 - )
  • Czech representative to the Program Commitee “Ideas” of 7th FP (2006-2013 )
  • Pool of Experts to evaluate scientific proposals, European Commission FP6, FP7, H2020, Brussels (2004-)
  • National D.Sc. defense boards in organic chemistry (member) and physical chemistry (vice-chairman) (2003 - )
  • Board of Directors, Czech Chemical Society (2001-2013)
  • National committee of the Czech Chemical Society (2001-2013 )
  • Member of government commission that is taking decisions about accreditation of university study programs in Chemistry (2000-2016)
  • Chairman of the Brno branch of the Czech Chemical Society (1997-2011)
  • Member of the American Chemical Society (1994 - )
  • Scientific Secretary of the Brno branch of the Czech Chemical Society (1993 - 1997)
Most significant professional accomplishments
  • Fellowship of Norwegian Royal Council for Scientific and Industrial Research (2 years), other fellowships to visit and teach at foreign universities (Rennes, Athens, Grenoble), several invited lectures on international meetings, organizing The Meeting of the Czech and Slovak Chemical Societies-chairman of the committee, co-organizing symposia on computational chemistry
Selected publications ( More on Researcher ID E-4460-2012)
  • TRNKA, Tomáš, Igor TVAROŠKA and Jaroslav KOČA. Automated Training of ReaxFF Reactive Force Fields for Energetics of Enzymatic Reactions. Journal of Chemical Theory and Computation. Washington DC: American Chemical Society, 2018, vol. 14, No 1, p. 291-302. ISSN 1549-9618. Available from: https://dx.doi.org/10.1021/acs.jctc.7b00870. URL info
  • HOUSER, Josef, Stanislav KOZMON, Deepti MISHRA, Sushil Kumar MISHRA, Patrick R ROMANO, Michaela WIMMEROVÁ and Jaroslav KOČA. Influence of Trp flipping on carbohydrate binding in lectins. An example on Aleuria aurantia lectin AAL. Plos one. San Francisco: Public Library of Science, 2017, vol. 12, No 12, p. 0189375-189391. ISSN 1932-6203. Available from: https://dx.doi.org/10.1371/journal.pone.0189375. URL info
  • TRISTAO RAMOS, Ravi José, Allan Cézar DE AZEVEDO MARTINS, Gabrielle DA SILVA DELGADO, Crina-Maria IONESCU, Peter Turán ÜRMÉNYI, Rosane SILVA and Jaroslav KOČA. CrocoBLAST: Running BLAST efficiently in the age of next-generation sequencing. Bioinformatics. Oxford: Oxford University Press, 2017, vol. 33, No 22, p. 3648-3651. ISSN 1367-4803. Available from: https://dx.doi.org/10.1093/bioinformatics/btx465. URL info
  • PRAVDA, Lukáš, David SEHNAL, Radka SVOBODOVÁ VAŘEKOVÁ and Jaroslav KOČA. Detekce biomolekulárních substruktur pomocí PatternQuery. In ENBIK - Národní bioinformatická konference. 2016. ISBN 978-80-7080-960-0. info
  • STŘELCOVÁ, Zora, Petr KULHÁNEK, Martin FRIÁK, Helge-Otto FABRITIUS, Michal PETROV, Joerg NEUGEBAUER and Jaroslav KOČA. The structure and dynamics of chitin nanofibrils in an aqueous environment revealed by molecular dynamics simulations. RSC Advances. Cambridge: Royal Society of Chemistry, 2016, vol. 6, No 36, p. 30710-30721. ISSN 2046-2069. Available from: https://dx.doi.org/10.1039/c6ra00107f. URL info
  • RAČEK, Tomáš, Jana PAZÚRIKOVÁ, Radka SVOBODOVÁ VAŘEKOVÁ, Stanislav GEIDL, Aleš KŘENEK, Francesco Luca FALGINELLA, Vladimír HORSKÝ, Václav HEJRET and Jaroslav KOČA. NEEMP: software for validation, accurate calculation and fast parameterization of EEM charges. Journal of Cheminformatics. London: BIOMED CENTRAL LTD, 2016, vol. 8, October, p. nestránkováno, 14 pp. ISSN 1758-2946. Available from: https://dx.doi.org/10.1186/s13321-016-0171-1. URL info
  • KUMARI, Manju, Stanislav KOZMON, Petr KULHÁNEK, Jakub ŠTĚPÁN, Igor TVAROŠKA and Jaroslav KOČA. Reaction Mechanism of O-GlcNAc Transferase Explored By QM/MM Molecular Dynamics. 2016. info
  • JANOŠ, Pavel, Stanislav KOZMON, Igor TVAROŠKA and Jaroslav KOČA. The GlcNAc-TV Glycosyltransferase Homology Model Strucutre. 2016. info
  • OPPELT, Jan, Jaroslav KOČA and Marek MRÁZ. Regulation of microRNA expression based on their common factors and properties. In CEITEC PhD retreat. 2015. ISBN 978-80-210-7825-3. URL info
  • PRAVDA, Lukáš, Karel BERKA, Radka SVOBODOVÁ VAŘEKOVÁ, David SEHNAL, Crina-Maria IONESCU, Michal OTYEPKA and Jaroslav KOČA. Anatomy of protein channels. In CEITEC PhD Retreat, Valtice, The Czech Republic. 2015. ISBN 978-80-210-7825-3. URL info
  • TRNKA, Tomáš, Stanislav KOZMON, Igor TVAROŠKA and Jaroslav KOČA. Stepwise Catalytic Mechanism via Short-Lived Intermediate Inferred from Combined QM/MM MERP and PES Calculations on Retaining Glycosyltransferase ppGalNAcT2. PLoS Computational Biology. SAN FRANCISCO: PUBLIC LIBRARY SCIENCE, 2015, vol. 11, No 4, p. "nestránkováno", 21 pp. ISSN 1553-734X. Available from: https://dx.doi.org/10.1371/journal.pcbi.1004061. URL info
  • SVOBODOVÁ VAŘEKOVÁ, Radka, Lukáš PRAVDA, David SEHNAL, Crina-Maria IONESCU and Jaroslav KOČA. MotiveQuery: Web application for fast detection of biomacromolecular fragments in the entire Protein Data Bank. In ISMB/ECCB 2015, Dublin, Ireland. 2015. URL info
  • MISHRA, Sushil Kumar, Gaetano CALABRO, Hannes H. LOEFFLER, Julien MICHEL and Jaroslav KOČA. Evaluation of Selected Classical Force Fields for Alchemical Binding Free Energy Calculations of Protein-Carbohydrate Complexes. Journal of Chemical Theory and Computation. Washington D.C.: American Chemical Society, 2015, vol. 11, No 7, p. 3333-3345. ISSN 1549-9618. Available from: https://dx.doi.org/10.1021/acs.jctc.5b00159. URL info
  • IONESCU, Crina-Maria, David SEHNAL, Francesco Luca FALGINELLA, Purbaj PANT, Lukáš PRAVDA, Tomáš BOUCHAL, Radka SVOBODOVÁ VAŘEKOVÁ, Stanislav GEIDL and Jaroslav KOČA. AtomicChargeCalculator: Interactive Web-based calculation of atomic charges in large biomolecular complexes and drug like molecules. Journal of Cheminformatics. London: BIOMED CENTRAL LTD, 2015, vol. 7, No 50, p. "nestránkováno", 13 pp. ISSN 1758-2946. Available from: https://dx.doi.org/10.1186/s13321-015-0099-x. URL info
  • GEIDL, Stanislav, Tomáš BOUCHAL, Tomáš RAČEK, Radka SVOBODOVÁ VAŘEKOVÁ, Václav HEJRET, Aleš KŘENEK, Ruben ABAGYAN and Jaroslav KOČA. High-quality and universal empirical atomic charges for chemoinformatics applications. Journal of Cheminformatics. London: BIOMED CENTRAL LTD, 2015, vol. 7, DEC, p. 1-10. ISSN 1758-2946. Available from: https://dx.doi.org/10.1186/s13321-015-0107-1. URL info
  • KUMARI, Manju, Stanislav KOZMON, Petr KULHÁNEK, Jakub ŠTĚPÁN, Igor TVAROŠKA and Jaroslav KOČA. Exploring Reaction Pathways for O-GlcNAc Transferase Catalysis. A String Method Study. Journal of Physical Chemistry B. WASHINGTON: AMER CHEMICAL SOC, 2015, vol. 119, No 12, p. 4371-4381. ISSN 1520-6106. Available from: https://dx.doi.org/10.1021/jp511235f. URL info
  • STADLBAUER, Petr, Petra KUHROVÁ, Pavel BANÁŠ, Jaroslav KOČA, Giovanni BUSSI, Lukáš TRANTÍREK, Michal OTYEPKA and Jiří ŠPONER. Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations. Nucleic Acids Research. Oxford: Oxford University Press, 2015, vol. 43, No 20, p. 9626-9644. ISSN 0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkv994. URL info
  • BÁRTOVÁ, Iveta, Jaroslav KOČA and Michal OTYEPKA. Functional Flexibility of Human Cyclin-Dependent Kinase-2 and Its Evolutionarily Conservation. Protein Science. COLD SPRING HARBOR LAB PRESS, 2008, vol. 17, No 1, p. 22-33. ISSN 0961-8368. info
  • MATOUŠEK, Jiří, Michal ČAJAN, Petr KULHÁNEK and Jaroslav KOČA. Mechanism of Hydrogen Bond Array Isomerization in Tetrahydroxycalix[4]arene and Tetrahydroxythiacalix[4]arene. Journal of Physical Chemistry A. USA: The American Chemical Society, 2008, vol. 112, No 1, p. 1076-1084. ISSN 1089-5639. info
  • MISHRA, Navnit Kumar, Petr KULHÁNEK, Lenka ŠNAJDROVÁ, Martin PETŘEK, Anne IMBERTY and Jaroslav KOČA. Molecular dynamics study of Pseudomonas eruginosa lectin-II complexed with monosaccharides. Proteins: Structure, Function, and Bioinformatics. Wiley, 2008, vol. 72, No 1, p. 382–392. ISSN 0887-3585. info
  • PROKOP, Martin, Jan ADAM, Zdeněk KŘÍŽ, Michaela WIMMEROVÁ and Jaroslav KOČA. TRITON: a graphical tool for ligand-binding protein engineering. Bioinformatics. Oxford University Press, 2008, vol. 24, No 17, p. 1955-1956. ISSN 1367-4803. Abstract and full text (open access artcle) Web page of the program TRITON info
  • BÁRTOVÁ, Iveta, Jaroslav KOČA and Michal OTYEPKA. Regulatory Phosphorylations of Cyclin-Dependent Kinase 2: An Insight from the Molecular Dynamics Simulations. Journal of Molecular Modeling. 2008, vol. 14, No 8, p. 761-768. ISSN 1610-2940. info
  • JIROUŠKOVÁ, Zuzana, Radka SVOBODOVÁ VAŘEKOVÁ, Jakub VANĚK and Jaroslav KOČA. Software news and updates: Electronegativity equalization method: Parameterization and validation for organic molecules using the Merz-Kollman-Singh charge distribution scheme (Software news and updates electronegativity equalization method: Parameterization and validation for organic molecules using the Merz-Kollman-Singh charge distribution scheme). Journal of Computational Chemistry. New York: John Wiley & Sons, 2008, vol. 2009, No 30, p. 1174-1178. ISSN 0192-8651. info
  • RÁZGA, Filip, Jaroslav KOČA, Ali MOKDAD and Jiří ŠPONER. Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA. Nucleic Acids Research. Oxford, UK: Oxford Press, 2007, vol. 35, No 12, p. 4007–4017. ISSN 0305-1048. info
  • PETŘEK, Martin, Pavlína KOŠINOVÁ, Jaroslav KOČA and Michal OTYEPKA. MOLE: A Voronoi Diagram-based Explorer of Molecular Channels, Pores and Tunnels. Structure. 2007, vol. 15, No 15, p. 1357-1363. ISSN 0969-2126. MOLE page info
  • BRETON, Christelle, Lenka ŠNAJDROVÁ, Charlotte JEANNEAU, Jaroslav KOČA and Anne IMBERTY. Structures and mechanisms of glycosyltransferases. Glycobiology. Oxford: Oxford University Press, 2006, vol. 16, No 2, p. 29R-37R, 9 pp. ISSN 0959-6658. Database of three-dimensional structures of glycosyltransferases info
  • MATOUŠEK, Jiří, Petr KULHÁNEK, Michal ČAJAN and Jaroslav KOČA. Effect of Solvation on Pinched Cone-Pinched Cone Interconversion of Tetraethoxycalix[4]arene and Tetraethoxythiacalix[4]arene. Journal of Physical Chemistry A. 2006, vol. 110, No 3, p. 861-867. ISSN 1089-5639. info
  • RÁZGA, Filip, Martin ZACHARIAS, Kamila RÉBLOVÁ, Jaroslav KOČA and Jiří ŠPONER. RNA kink-turns as molecular elbows: Hydration, cation binding, and large-scale dynamics. Structure. USA: CELL PRESS, 1100 MASSACHUSETTS AVE, CAMB, 2006, vol. 14, No 5, p. 825-835, 10 pp. ISSN 0969-2126. info
  • OTYEPKA, Michal, Iveta BÁRTOVÁ, Zdeněk KŘÍŽ and Jaroslav KOČA. DIFFERENT MECHANISMS OF CDK5 AND CDK2 ACTIVATION AS REVEALED BY CDK5/P25 AND CDK2/CYCLIN A DYNAMICS. The Journal of biological chemistry. 2006, vol. 281, No 11, p. 7271-7281. ISSN 0021-9258. info
  • SVOBODOVÁ VAŘEKOVÁ, Radka and Jaroslav KOČA. Optimized and parallelized implementation of the electronegativity equalization method and the atom-bond electronegativity equalization method. J Comput Chem. 2006, vol. 27, No 3, p. 396-405. ISSN 0192-8651. info
  • RÉBLOVÁ, Kamila, Filip LANKAŠ, Filip RÁZGA, Maryna V KRASOVSKA, Jaroslav KOČA and Jiří ŠPONER. Structure, Dynamics, and Elasticity of Free 16S rRNA Helix 44 Studied by Molecular Dynamics Simulations. Biopolymers. USA: Wiley InterScience, 2006, vol. 82, No 5, p. 504-520. ISSN 0006-3525. info
  • BÁRTOVÁ, Iveta, Michal OTYEPKA, Zdeněk KŘÍŽ and Jaroslav KOČA. 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. Protein Science. COLD SPRING HARBOR LAB PRESS, 2005, vol. 14, No 2, p. 445-451. ISSN 0961-8368. info
  • RÁZGA, Filip, Jaroslav KOČA, Jiří ŠPONER and Neocles B. LEONTIS. Hinge-Like Motions in RNA Kink-Turns: The Role of the Second A-minor Motif and Nominally Unpaired Bases. Biophysical Journal. USA: Biophysical Society, 2005, vol. 88, No 5, p. 3466-3485. ISSN 0006-3495. info
  • KULHÁNEK, Petr, Milan POTÁČEK and Jaroslav KOČA. Quantum-chemical insight into mechanism of combined intra-intermolecular cycloaddition. Collection of Czechoslovak Chemical Communications. Prague, 2004, 69/2004, No 1, p. 231-241. ISSN 0010-0765. info
  • ŠNAJDROVÁ, Lenka, Petr KULHÁNEK, Anne IMBERTY and Jaroslav KOČA. Molecular dynamics simulations of glycosyltransferase LgtC. Carbohydrate Research. 2004, vol. 339, No 5, p. 995-1006. ISSN 0008-6215. Science Direct - Carbohydrate Research: Molecular dynamics simulations of glycosyltransferase LgtC info
  • KŘÍŽ, Zdeněk, Michal OTYEPKA, Iveta BÁRTOVÁ and Jaroslav KOČA. Analysis of CDK2 active-site hydration: A method to design new inhibitors. Proteins: Structure, Function, and Bioinformatics. Wiley, 2004, vol. 55, No 3, p. 258-274. ISSN 0887-3585. info
  • NAVRÁTILOVÁ, Hana, Radka OPATŘILOVÁ, Zdeněk KŘÍŽ and Jaroslav KOČA. Enantioselective chromatography and molecular modeling of novel aryloxyaminopropan-2-ols with the alkyl carbamate function. Chirality. 2004, vol. 16, No 3, p. 139-146. ISSN 0899-0042. info
  • RÁZGA, Filip, Naďa ŠPAČKOVÁ, Kamila RÉBLOVÁ, Jaroslav KOČA, Neocles B. LEONTIS and Jiří ŠPONER. Ribosomal RNA Kink-turn Motif - A Flexible Molecular Hinge. Journal of Biomolecular Structure & Dynamics. Adenine Press, 2004, vol. 22, No 2, p. 183-193. ISSN 0739-1102. info
  • FADRNÁ, Eva, Naděžda ŠPAČKOVÁ, Richard ŠTEFL, Jaroslav KOČA, Thomas E. CHEATHAM and Jiří ŠPONER. Molecular dynamics simulations of guanine quadruplex loops:Advances and force field limitations. Biophysical Journal. Bethesda, USA: Biophysical Society, 2004, vol. 87, No 1, p. 227-242. ISSN 0006-3495. URL info
  • GIANLUCA, Cioci, Alain RIVET, Jaroslav KOCA and Serge PEREZ. Conformational Analysis of Complex Oligosaccharides: The CICADA Approach to the Uromodulin O-Glycans. Carbohydrate Research. 2004, vol. 339, No 4, p. 949-959. ISSN 0008-6215. info
  • RÉBLOVÁ, Kamila, Nadezda SPACKOVÁ, Jaroslav KOČA, Neocles LEONTIS and Jiri SPONER. Long-residency hydration, cation binding and dynamics of Loop E/Helix IV rRNA - L25 protein complex. Biophysical Journal. New York, USA: Rockefeller University, 2004, vol. 87, No 5, p. 3397-3412. ISSN 0006-3465. info
  • BÁRTOVÁ, Iveta, Michal OTYEPKA, Zdeněk KŘÍŽ and Jaroslav KOČA. Activation and Inhibition of Cyclin-Dependent Kinase-2 by Phosphorylation; A Molecular Dynamics Study Reveals the Functional Importance of the Glycine-Rich Loop. Protein Science. COLD SPRING HARBOR LAB PRESS, 2004, vol. 13, No 6, p. 1449-1457. ISSN 0961-8368. info
  • VRBKA, Luboš, Petr KLÁN, Zdeněk KŘÍŽ, Jaroslav KOČA and Peter J. WAGNER. Computer Modeling and Simulations on Flexible Bifunctional Systems: Intramolecular Energy Transfer Implications. Journal of Physical Chemistry A. USA: The American Chemical Society, 2003, vol. 107, No 18, p. 3404-3414. ISSN 1089-5639. info
  • FADRNÁ, Eva and Jaroslav KOČA. Conformational Flexibility of Two RNA Trimers Explored by Computational Tools and Database Search. Journal of Biomolecular Structure and Dynamics. USA: Adenine Press, 2003, vol. 20, No 5, p. 715-731. ISSN 0739-1102. URL info
  • KOČA, Jaroslav, Chang-Guo ZHAN, Robert RITTENHOUSE and Rick ORNSTEIN. Coordination number of zinc ions in the phosphotriesterase active site by molecular dynamics and quantum mechanics. Journal of Computational Chemistry. New York: John Wiley & Sons, 2003, vol. 24, No 3, p. 368-378. ISSN 0192-8651. info
  • RÉBLOVÁ, Kamila, Nadezda SPACKOVÁ, Richard STEFL, Kristina CSASZAR, Jaroslav KOCA, Neocles LEONTIS and Jiri SPONER. Non-Watson-Crick Basepairing and Hydration in RNA Motifs:. Biophysical Journal. New York, USA: Rockefeller University, 2003, vol. 84, No 6, p. 3564-3582, 18 pp. ISSN 0006-3465. info
  • KULHÁNEK, Petr, Edward W. SCHLAG and Jaroslav KOČA. Mechanism of Proton Transfer in Short Protonated Oligopeptides. 1. N-Methylacetamide and N2-Acetyl-N1-methylglycinamide. J. Phys. Chem. A. American Chemical Society, 2003, vol. 107, No 30, p. 5789-5797, 8 pp. ISSN 1089-5639. URL info
  • KŘÍŽ, Zdeněk, Jaroslav KOČA and Per H. J. CARLSEN. A Computer Program for the Simulation of the NOE Effect in NMR Spectroscopy, and Its Implementation into the CICADA Conformational Search Program (A Computer Program for the Simulation of the NOE Effect in NMR Spectroscopy, and Its Implemetation into the CICADA Conformational Search Program). Internet Electronic Journal of Molecular Design. BioChem Press, 2003, vol. 2, No 2, p. 55-69. ISSN 1538-6414. info
  • KŘÍŽ, Zdeněk, Jaroslav KOČA, Anne IMBERTY, Aurelia CHARLOT and Rachel AUZELY-VELTY. Investigation of the complexation of (+)-catechin by b-cyclodextrin by a combination of NMR, microcalorimetry and molecular modeling techniques (Investigation of the complexation of (+)-catechin by b-cyclodextrin by a combination of NMR, microcalorimetry and molecular modeling techniques). Organic and Biomolecular Chemistry. Royal Society of Chemistry, 2003, vol. 1, No 14, p. 2590-2595. ISSN 1477-0520. info
  • ŠTEFL, Richard, Thomas E. CHEATHAM, Naděžda ŠPAČKOVÁ, Eva FADRNÁ, Imre BERGER, Jaroslav KOČA and Jiří ŠPONER. Formation Pathways of a Guanine-Quadruplex DNA Revealed by Molecular Dynamics and Thermodynamics Analysis of the Substates. Biophysical Journal. Bethesda, USA: Biophysical Society, 2003, vol. 85, No 3, p. 1787-1804. ISSN 0006-3495. URL info
  • KULHÁNEK, Petr, Edward W. SCHLAG and Jaroslav KOČA. A Novel Mechanism of Proton Transfer in Protonated Peptides. Journal of the American Chemical Society. Washington, DC., USA: American Chemical Society, 2003, vol. 125, No 45, p. 13678-13679, 1 pp. ISSN 0002-7863. URL info
  • RÉBLOVÁ, Kamila, Naděžda ŠPAČKOVÁ, Judit ŠPONER, Jaroslav KOČA and Jiři ŠPONER. Molecular dynamics simulations of RNA kissing loop motifs reveal structural dynamics and formation of cation-binding pockets. Nucleic Acids Research. Oxford University Press, 2003, vol. 31, No 23, p. 6942-6952. ISSN 0006-3465. info
  • ČAJAN, Michal, Pavel LHOTÁK, Jan LANG, Hana DVOŘÁKOVÁ, Ivan STIBOR and Jaroslav KOČA. The conformational behaviour of thiacalix[4]arenes: the pinched cone/pinched cone transition. Journal of the chemical society. Perkin transactions II, Physical organic chemistry. London: Chemical society, 2002, vol. 100, No 1, p. 1922-1929. ISSN 1472-779X. info
  • OTYEPKA, Michal, Zdeněk KŘÍŽ and Jaroslav KOČA. Dynamics and binding modes of free cdk2 and its two complexes with inhibitors studied by computer simulations. Journal of Biomolecular Structure & Dynamics. GUILDERLAND: ADENINE PRESS, 2002, vol. 20, No 2, p. 141-154. ISSN 0739-1102. info
  • BOHÁČ, Michal, Yuji NAGATA, Zbyněk PROKOP, Martin PROKOP, Marta MONINCOVÁ, Masataka TSUDA, Jaroslav KOČA and Jiri DAMBORSKÝ. Halide-stabilizing residues of haloalkane dehalogenases studied by quantum mechanic calculations and site-directed mutagenesis. Biochemistry. 2002, vol. 41, No 48, p. 14272-14280. ISSN 0006-2960. URL info
  • DAMBORSKÝ, Jiří, Martin PROKOP and Jaroslav KOČA. TRITON: graphic software for rational engineering of enzymes. Trends in Biochemical Sciences. 2001, vol. 28, No 1, p. 71-73. URL info
  • KOČA, Jaroslav, Chang-Guo ZHAN, Robert RITTENHOUSE and Rick ORNSTEIN. Mobility of the Active Site bound Paraoxon and Sarin in Zinc-Phosphotriesterase by Molecular Dynamics Simulation and Quantum (Mobility of the Active Site bound Paraoxon and Sarin in Zinc-Phosphotriesterase by Molecular Dynamics Simulation and Qunatum). Journal of the American Chemical Society. Washington, D.C.: American Chemical Society, 2001, vol. 123, No 1, p. 817-826. ISSN 0002-7863. info
  • ŠTEFL, Richard, Lukáš TRANTÍREK, Michaela VORLÍČKOVÁ, Jaroslav KOČA, Vladimír SKLENÁŘ and Jaroslav KYPR. A-like Guanine-Guanine Stacking in the Aqueous DNA. Journal of Molecular Biology. USA: Academic Press, 2001, vol. 307, No 1, p. 513-524. ISSN 0022-2836. info
  • PETROVÁ, Pavla, Celine MONTEIRO, Catherine HERVE DU PENHOAT, Jaroslav KOČA and Anne IMBERTY. Conformational behavior of nucleotide-sugar in solution: Molecular dynamics and NMR study of solvated uridinediphosphate-glucose in the presence of monovalent cations. Biopolymers. John Wiley & Sons, Inc, 2001, vol. 58, No 7, p. 617-635. ISSN 0006-3525. info
  • KŘÍŽ, Zdeněk, Per H.J. CARLSEN and Jaroslav KOČA. Conformational features of linear and cyclic enkephalins. A computational study. Journal of Molecular Structure (Theochem). Netherlands: Elsevier Science, 2001, vol. 540, No 1, p. 231-250. ISSN 0166-1280. info
  • SITKOVÁ, Pavla, Jaroslav KOČA and Anne IMBERTY. Molecular dynamics simulations of solvated UDP-glucose in interaction with Mg cations. European Journal of Biochemistry. 2001, vol. 268, No 1, p. 5365-5374. info
  • ŠTEFL, Richard, Naděžda ŠPAČKOVÁ, Imre BERGER, Jaroslav KOČA and Jiří ŠPONER. Molecular dynamics of DNA quadruplex molecules containing inosine, 6-thioguanine and 6-thiopurine. Biophysical Journal. Bethesda, USA: Biophysical Society, 2001, vol. 80, No 1, p. 455-468. ISSN 0006-3495. info
  • TRANTÍREK, Lukáš, Richard ŠTEFL, Michalea VORLÍČKOVÁ, Jaroslav KOČA, Vladimír SKLENÁŘ and Jaroslav KYPR. An A-type Double Helix of DNA Having B-type Puckering of the Deoxyribose Rings. Journal of Molecular Biology. USA: Academic Press, 2000, vol. 297, No 4, p. 907-922. ISSN 0022-2836. info
  • ČAJAN, Michal, Jiří DAMBORSKÝ, Ivan STIBOR and Jaroslav KOČA. Stability of Complexes of Aromatic Amides with Bromide Anion: Quantitative Structure-Property Relationships. Journal of Chemical Information and Computer Sciences. Washington, DC: ACS, 2000, vol. 40, No 5, p. 1151-1157. ISSN 0095-2338. URL info
  • KOČA, Jaroslav, Martin LUDIN, Serge PEREZ and Anne IMBERTY. Single-coordinate-driving method for molecular docking: Application to modeling of guest inclusion in cyclodextrin. Journal of Molecular Graphics and Modelling. New York: Elsevier Science Inc., 2000, vol. 2000, No 18, p. 108-117. info
  • PROKOP, Martin, Jiří DAMBORSKÝ and Jaroslav KOČA. TRITON: in silico construction of protein mutants and prediction of their activities. Bioinformatics. 2000, vol. 16, No 9, p. 845-846. ISSN 1367-4803. URL info
  • ŠTEFL, Richard and Jaroslav KOČA. Unrestrained Molecular Dynamics Simulations of d(AT5]2 Duplex in Aqueous Solution: Hydration and Sodium Ions Binding in the Minor Groove. Journal of the American Chemical Society. Washington, D.C.: American Chemical Society, 2000, vol. 122, No 22, p. 5025-5033. ISSN 0002-7863. info
  • OTYEPKA, Michal, Vladimír KRYŠTOF, Libor HAVLÍČEK, Věra SIEGLEROVÁ, Miroslav STRNAD and Jaroslav KOČA. Docking-Based Development of Purine-like Inhibitors of Cyclin-Dependent Kinase 2. Journal of Medicinal Chemistry. American Chemical Society, 2000, vol. 43, No 13, p. 2506-2513. ISSN 0022-2623. info
  • PETROVÁ, Pavla, Jaroslav KOČA and Anne IMBERTY. Effect of Cation Concentration on Molecular Dynamics Simulations of UDP-glucose. (Effect of Cation Concentration on Molecular Dynamics Simulations of UDP-glucose). Molecular Simulations. 2000, vol. 24, No 1, p. 325-330. info
  • ŠTEFL, Richard, Eva FADRNÁ and Jaroslav KOČA. Differences in Conformational Behavior of ATA and TAT Sequences in Single Strand DNA Trimer. Journal of Biomolecular Structure and Dynamics. USA: Adenine Press, 1999, vol. 16, No 5, p. 1087-1095. ISSN 0739-1102. URL info
  • ČAJAN, Michal, Ivan STIBOR and Jaroslav KOČA. Computational Studies on the Stability of [Amide]Br- Complexes. Journal of Physical Chemistry A. USA: ACS, 1999, vol. 103, No 19, p. 3778-3782. ISSN 1089-5639. URL info
  • DAMBORSKÝ, Jiří and Jaroslav KOČA. Analysis of the reaction mechanism and substrate specificity of haloalkane dehalogenases by sequential and structural comparisons. Protein Engineering. 1999, vol. 12, No 11, p. 989-998. URL info
  • ČERNOHORSKÝ, Martin, M. VAULTIER and Jaroslav KOČA. Comparison of conformational behavior of the short alanine peptides and their boron analogues. Journal of Molecular Structure (Theochem). Amsterdam: Elsevier Science, 1999, vol. 489, 2--3, p. 213-224. ISSN 0166-1280. info
  • ČERNOHORSKÝ, Martin, Sofiane KETTOU and Jaroslav KOČA. VADER: New Software for Exploring Interconversions on Potential Energy Surface. J.Chem.Inf.Comput.Sci. 1999, vol. 39, No 4, p. 705-712. ISSN S0095-2338. info
  • LYNAM, Mary, Michal KUTÝ, Jiří DAMBORSKÝ, Jaroslav KOČA and Peter ADRIAENS. Molecular orbital calculations to describe microbial reductive dechlorination of polychlorinated dioxins. Environmental Toxicology and Chemistry. 1998, vol. 17, No 6, p. 988-997. URL info
  • DAMBORSKÝ, Jiří, Michal BOHÁČ, Martin PROKOP and Jaroslav KOČA. Computational site-directed mutagenesis of haloalkane dehalogenase in position 172. Protein Engineering. 1998, vol. 11, No 10, p. 901-907. URL info
  • KUTÝ, Michal, Jiří DAMBORSKÝ, Martin PROKOP and Jaroslav KOČA. A molecular modelling study of the catalytic mechanism of haloalkane dehalogenase: 2. Quantum chemical study of complete reaction mechanism. Journal of Chemical Information and Computer Sciences. 1998, vol. 38, No 4, p. 736-741. ISSN 0095-2338. URL info
  • GRŮZA, Jan, Jaroslav KOČA, Serge PÉREZ and Anne IMBERTY. Comparison of force-field parametrizations as applied to conformational analysis of ribofuranosides. Journal of Molecular Structure (Theochem). Netherlands: Elsevier Science, 1998, vol. 424, No 3, p. 269-280. ISSN 0166-1280. URL info
  • KOČA, Jaroslav. Kam se ubira pocitacova chemie - zaostreno na modelovani vetsich molekul (Where does computer chemistry move - focused on larger molecules modeling). Chemické listy. Praha: Česká společnost chemická, 1998, vol. 92, No 2, p. 101-113. ISSN 0009-2770. URL info
  • KOČA, Jaroslav. Travelling through conformational space: an approach for analyzing the conformational behaviour of flexible molecules. (Travelling through conformational space: an approach for analyzing the conformational behaviour of flexible molecules). Progress in Biophysics and Molecular Biology. 1998, vol. 70, No 2, p. 137-173. ISSN 0079-6107. info
  • ČERNOHORSKÝ, Martin, Michal KUTÝ and Jaroslav KOČA. A Multidimensional Driver for Quantum Chemistry Program MOPAC. Computers & Chemistry. Elsevier Science, 1997, vol. 21, No 1, p. 35-44. ISSN 0097-8485. info
  • CASSET, F., A. IMBERTY, C. HERVÉ DU PENTHOAT, Jaroslav KOČA and S. PERÉZ. Validation of two conformational searching methods applied to sucrose: simulation of NMR andchiro-optical data. Journal of Molecular Structure (Theochem). Amsterdam: Elsevier Science, 1997, 395-396, 1-3, p. 211-214. ISSN 0166-1280. info
  • FADRNÁ, Eva and Jaroslav KOČA. Single-coordinate-driving method combined with simulated annealing. An efficient tool to search conformational space. Journal of Physical Chemistry B. USA: ACS Publications, 1997, vol. 101, No 39, p. 7863-7868. ISSN 1089-5647. URL info
  • FADRNÁ, Eva and Jaroslav KOČA. A combination of driving method with simulated annealing to search conformational space. Journal of Molecular Structure (Theochem). Netherlands: Elsevier Science, 1997, vol. 398, No 399, p. 523-528. ISSN 0166-1280. URL info
  • DAMBORSKÝ, Jiří, Michal KUTÝ, Miroslav NĚMEC and Jaroslav KOČA. A molecular modelling study of the catalytic mechanism of haloalkane dehalogenase: 1. Quantum chemical study of the first reaction step (A molecular modelling study of the catalytic mechanism of haloalkane dehalogenase:1. Quantum chemical study of the first reaction step). Journal of Chemical Information and Computer Sciences. 1997, vol. 37, No 3, p. 562-568. ISSN 0048-3000. URL info
  • DAMBORSKÝ, Jiří, Michal KUTÝ, Miroslav NĚMEC and Jaroslav KOČA. Molecular modelling to understand the mechanisms of microbial degradation - application to hydrolytic dehalogenation with haloalkane dehalogenases. In QSAR in Environmental Sciences. 1st ed. Pensacola: SETAC Press, 1997, p. 5-24. URL info
  • STIBOR, Ivan, Dana S.M. HAFEED, Pavel LHOTÁK, Jana HODAČOVÁ, Jaroslav KOČA and Michal ČAJAN. From the Amide Bond Activation to Simultaneous Recognition of Anion-Cation Couple. Gazetta Chimica Italiana. Itálie: Societa Chimica Italiana, 1997, vol. 127, No 11, p. 673-685. ISSN 0016-5603. info
  • FADRNÁ, Eva and Jaroslav KOČA. CICADA Interface with AMBER. An Application on Oligonucleotides and their Fragments. Journal of Biomolecular Structure and Dynamics. USA: Adenine Press, 1996, vol. 14, No 1, p. 137-152. ISSN 0739-1102. URL info
  • KŘÍŽ, Zdeněk, Jaroslav KOČA and Per H. J. CARLSEN. Conformational Behavior and Flexibility of Terminally Blocked Cysteine and Cystine. J. Mol. Mod. Nemecko: Springer-Verlag, 1996, vol. 2, No 3, p. 51-61. ISSN 0948-5023. URL info
  • ENGELSEN, Soren b., Jaroslav KOČA and Isabelle BRACCINI. Travelling on the potential energy surfaces of carbohydrates: comparative application of an exhaustive systematic conformational search with an heuristic search. Carbohydrate Research. 1995, vol. 276, No 1, p. 1-29. ISSN 0008-6215. info
  • IMBERTY, A., E. MIKROS and Jaroslav KOČA. Computer Simulation of Histo-Blood Group Oligosacharides. Glycoconjugate Journal. 1995, vol. 12, No 1, p. 331-349. ISSN 0282-0080. info
  • KOČA, Jaroslav, Serge PÉREZ and Anne IMBERTY. Conformational Analysis and Flexibility of Carbohydrates Using the CICADA Approach with MM3. Journal of computational chemistry : organic, inorganic, physical, biological. New York: John Wiley & Sons, 1995, vol. 16, No 3, p. 296-310. ISSN 0192-8651. info
  • KOČA, Jaroslav and Per CARLSEN. Conformational behavior and flexibility of met-enkephalin. Journal of Molecular Structure (Theochem). Amsterdam: Elsevier Science, 1995, vol. 337, No 1, p. 17-24. ISSN 0166-1280. info
  • KOČA, Jaroslav. Computer simulation of conformational movement based on interconversion phenomena. Journal of Molecular Structure (Theochem). Amsterdam: Elsevier Science, 1995, vol. 343, No 1, p. 125-132. ISSN 0166-1280. info
  • MATYSKA, Luděk and J. KOČA. D-CICADA - a software for confomational PES Elucidation on network of workstations. Journal of computational chemistry. New York: John Wiley & Sons, 1994, vol. 1994, No 15, p. 937-946. ISSN 0192-8651. info
  • KOČA, Jaroslav. A Computer Program CICADA-Travelling Along Conformational Potential Energy Hypersurface. Journal of Molecular Structure (Theochem). Amsterdam: Elsevier Science, 1994, vol. 1994, No 1, p. 13-24. ISSN 0166-1280. info
  • KOČA, Jaroslav, Zdeněk KŘÍŽ and P.H.J. CARLSEN. A Computer Study of Conformational Flexibility of 20 Common Amino Acids. Journal of Molecular Structure. Nizozemsko: Elsevier Science, 1994, vol. 306, No 1, p. 157-164. ISSN 0022-2860. info
  • MATYSKA, Luděk and Jaroslav KOČA. D-CICADA, a Software for Conformational PES Elucidation on Network of Workstations. Journal of computational chemistry : organic, inorganic, physical, biological. New York: John Wiley & Sons, 1994, vol. 1994, No 1, p. 937-946. ISSN 0192-8651. info
  • MATYSKA, Luděk and Milan KRATOCHVÍL. Logická struktura chemie. 1. vyd. Brno: Masarykova univerzita v Brně, 1993, 181, xxxii. ISBN 8021008946. info
  • HLADKÁ, Eva, Jaroslav KOČA, Milan KRATOCHVÍL, Vladimír KVASNIČKA, Luděk MATYSKA, Jiří POSPÍCHAL and Vladimir POTUCEK. Synthon Model and Program PEGAS for Computer Assisted Organic Synthesis. Heidelberg: Springer-Verlag, 1993, 320 pp. Computer Chemistry, Topics in Current Chemistry. ISBN 3-540-55902-7. info
  • HLADKÁ, Eva, Jaroslav KOČA and Milan KRATOCHVÍL. The Synthon Model and the Program PEGAS for Computer Assisted Organic Synthesis. Top. Cur. Chem. Springer-Verlag, Berlin. Berlin: Springer-Verlag, 1993, vol. 166, No 1, p. 121-197. ISSN 0340-1022. info
  • KOČA, Jaroslav. Potential energy hypersurface and molecular flexibility. Journal of Molecular Structure. 1993, vol. 291, No 1, p. 255-269. ISSN 0022-2860. info
  • KOČA, Jaroslav and Per CARLSEN. Conformational behavior and flexibility of terminally blocked alanine di- and tripeptides. Journal of Molecular Structure. 1993, vol. 291, No 1, p. 271-286. ISSN 0022-2860. info
  • KOČA, Jaroslav. Synthon Model of Organic Chemistry and Synthesis Design. Edited by G. Berthier. Berlin: Springer-Verlag, 1989, 207 s. ISBN 3540509321. info
  • KVASNIČKA, Vladimír, Milan KRATOCHVÍL and Jaroslav KOČA. Matematická chemie a počítačové řešení syntéz. 1. vyd. Praha: Academia, 1987, 149 s. info
  • KOČA, Jaroslav, Josef HAVEL and Ivan NOVOTNÝ. Základy programování a chemometrie. 1. vyd. Praha: Státní pedagogické nakladatelství, 1987, 243 s. info

2017/08/22

Curriculum vitae: prof. RNDr. Jaroslav Koča, DrSc. (učo 610), version: English(1), last update: 2017/08/22 10:17, J. Koča