Prof. RNDr. Jaroslav Koča, DrSc.
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MISHRA, Sushil Kumar - KOČA, Jaroslav.
Free energy calculation in lectin/saccharide complexes. 2012.
MISHRA, Sushil Kumar - DEMO, Gabriel - KOČA, Jaroslav - WIMMEROVÁ, Michaela.
In Silico Engineering of Proteins that Recognize Small Molecules. In Protein Engineering. Neuveden : InTech - Open Access Publisher, 2012. Neuveden, ISBN 978-953-510-037-9, pp. 307-344.
KRIŠTOFÍKOVÁ, Zdena - KŘÍŽ, Zdeněk - ŘÍPOVÁ, Daniela - KOČA, Jaroslav.
Interactions of Amyloid beta Peptide 1 - 40 and Cerebrosterol. Neurochemical Research, New York, Kluwer Academic /Plenum Publ/, USA. ISSN 0364-3190, 2012, vol. 37, no. 3, pp. 604-613.
SEHNAL, David - SVOBODOVÁ VAŘEKOVÁ, Radka - HUBER, Heinrich J. - GEIDL, Stanislav - IONESCU, Crina-Maria - WIMMEROVÁ, Michaela - KOČA, Jaroslav.
SiteBinder: An improved approach for comparing multiple protein structural motifs. Journal of Chemical Information and Modeling, USA. ISSN 1549-9596, 2012, vol. 52, no. 2, 343–359-17 pp.
WIESNER, Jiří - KOČA, Jaroslav.
Calculating pKa of selected active site aminoacids in acetylcholinesterase. 2011.
KOZMON, Stanislav - MATUŠKA, Radek - SPIWOK, Vojtěch - KOČA, Jaroslav.
Carbohydrate CH/pi interactions – Theoretical investigation of the favourable regions in the carbohydrate surroundings. 2011.
SVOBODOVÁ VAŘEKOVÁ, Radka - SEHNAL, David - PRAVDA, Lukáš - OPPELT, Jan - IONESCU, Crina-Maria - GEIDL, Stanislav - KOČA, Jaroslav.
Comparison of protein structural motifs – challenges and algorithms. Improved approach and case studies. 2011.
STŘELCOVÁ, Zora - ŠTĚPÁN, Jakub - KULHÁNEK, Petr - CARLONI, Paolo - KOČA, Jaroslav.
Computational study of the dimethylphosphate hydrolysis as the reference system for the understanding of the restriction endonucleases mechanism. 2011.
KOZMON, Stanislav - MATUŠKA, Radek - SPIWOK, Vojtech - KOČA, Jaroslav.
Dispersion interactions of carbohydrates with condensate aromatic moieties: Theoretical study on the CH–pi interaction additive properties. Physical Chemistry Chemical Physics, Great Britain, ROYAL SOC CHEMISTRY, Great Britain. ISSN 1463-9076, 2011, vol. 13, no. 31, pp. 14215-14222.
RYŠKA, Jan - MISHRA, Sushil Kumar - SVOBODOVÁ VAŘEKOVÁ, Radka - KOČA, Jaroslav.
Docking study of matrix metalloproteinase inhibitors. 2011.
MISHRA, Sushil Kumar - SUND, Johan - AQVIST, Johan - KOČA, Jaroslav.
Fast and Accurate calculation of Lectin/Saccharide Binding Free Energy. 2011.
IONESCU, Crina-Maria - SVOBODOVÁ VAŘEKOVÁ, Radka - SEHNAL, David - SKŘEHOTA, Ondřej - KOČA, Jaroslav.
Fast methods of atomic charge calculation: the Electronegativity Equalization Method for proteins. 2011.
GEIDL, Stanislav - BERÁNEK, Roman - SVOBODOVÁ VAŘEKOVÁ, Radka - BOUCHAL, Tomáš - BRUMOVSKÝ, Miroslav - KUDERA, Michal - SKŘEHOTA, Ondřej - KOČA, Jaroslav.
How the methodology of 3D structure preparation influences the quality of QSPR models?. 2011.
MISHRA, Sushil Kumar - ALÁN, Jan - KULHÁNEK, Petr - KOČA, Jaroslav.
How to calculate binding energy in Protein-Carbohydrate complexes. 2011.
WIESNER, Jiří - KOČA, Jaroslav.
pKa Calculation for Selected Active Site Residues in Acetylcholinesterase. 2011. ISBN 978-80-7378-180-4.
KULHÁNEK, Petr - MONES, Letif - STŘELCOVÁ, Zora - SIMON, Istvan - FUXREITER, Monika - KOČA, Jaroslav.
PMFLib – A TOOLKIT FOR FREE ENERGY CALCULATIONS. 2011.
KULHÁNEK, Petr - MONES, Letif - STŘELCOVÁ, Zora - SIMON, Istvan - FUXREITER, Monika - KOČA, Jaroslav.
PMFLib – A TOOLKIT FOR FREE ENERGY CALCULATIONS II. 2011.
SVOBODOVÁ VAŘEKOVÁ, Radka - GEIDL, Stanislav - IONESCU, Crina-Maria - SKŘEHOTA, Ondřej - KUDERA, Michal - SEHNAL, David - BOUCHAL, Tomáš - ABAGYAN, Ruben A. - HUBER, Heinrich J. - KOČA, Jaroslav.
Predicting pK(a) values of substituted phenols from atomic charges: Comparison of different quantum mechanical methods and charge distribution schemes. Journal of Chemical Information and Modeling, USA. ISSN 1549-9596, 2011, vol. 51, no. 8, 1795–1806-12 pp.
GEIDL, Stanislav - SVOBODOVÁ VAŘEKOVÁ, Radka - SKŘEHOTA, Ondřej - KUDERA, Michal - IONESCU, Crina-Maria - SEHNAL, David - BOUCHAL, Tomáš - KOČA, Jaroslav.
Predicting pKa values of substituted phenols from atomic charges. 2011.
POKORNÁ, Martina - ADAM, Jan - SABIN, Charles - MITCHELL, Edward P. - IMBERTY, Anne - KOČA, Jaroslav - WIMMEROVÁ, Michaela.
Production of Ca-dependent high-affinity lectins with defined specificity by mutagenesis of PA-IIL lectin. 2011.
POKORNÁ, Martina - ADAM, Jan - MRÁZKOVÁ, Jana - KOČA, Jaroslav - WIMMEROVÁ, Michaela.
Protein engineering of lectins - in silico and in vitro approaches. 2011.
SKŘEHOTA, Ondřej - SVOBODOVÁ VAŘEKOVÁ, Radka - GEIDL, Stanislav - IONESCU, Crina-Maria - JAN, Žídek - KOČA, Jaroslav.
QSPR Designer – Employ your own descriptors in the automated QSAR modeling process. 2011.
SKŘEHOTA, Ondřej - SVOBODOVÁ VAŘEKOVÁ, Radka - GEIDL, Stanislav - KUDERA, Michal - SEHNAL, David - IONESCU, Crina-Maria - BOUCHAL, Tomáš - KOČA, Jaroslav.
QSPR modeling – algorithms, challenges and IT solutions. 2011.
Reaction Mechanism of MutH Enzyme - Quantum Mechanics/Molecular Mechanics Study 2. 2011. přednáška na konferenci Setkani Biochemiku. ISBN 978-80-210-5594-0.
JAISWAL, Deepti - SVOBODOVÁ VAŘEKOVÁ, Radka - IONESCU, Crina-Maria - SEHNAL, David - KOČA, Jaroslav.
Searching for tunnels of proteins - comparison of approaches and available software tools. 2011.
SEHNAL, David - SVOBODOVÁ VAŘEKOVÁ, Radka - HUBER, Heinrich J. - GEIDL, Stanislav - IONESCU, Crina-Maria - WIMMEROVÁ, Michaela - KOČA, Jaroslav.
SiteBinder – an improved approach for comparing multiple protein structural motifs. Case studies on biologically important motifs. 2011.
SiteBinder – an improved software superimposing multiple protein structural motifs and its applications. 2011. ISBN 978-80-210-5594-0.
KŘÍŽ, Zdeněk - KRIŠTOFÍKOVÁ, Zdena - KOČA, Jaroslav.
Study of interactions of 24(S,R)-hydroxycholesterols with 1-42 amyloid beta using molecular modeling methods. 2011.
KOZMON, Stanislav - MATUŠKA, Radek - SPIWOK, Vojtěch - KOČA, Jaroslav.
STUDY OF THE CARBOHYDRATE CH/pi INTERACTIONS FAVOURABLE REGIONS IN THE CARBOHYDRATE SURROUNDINGS. 2011.
KOZMON, Stanislav - MATUŠKA, Radek - SPIWOK, Vojtěch - KOČA, Jaroslav.
Systematic Study of Carbohydrate-Aromatic CH-pi Dispersion Interaction by DFT and Highly Correlated Ab Initio Methods. 2011.
KOZMON, Stanislav - MATUŠKA, Radek - SPIWOK, Vojtěch - KOČA, Jaroslav.
THEORETICAL INVESTIGATION OF THE CARBOHYDRATE CH/pi INTERACTIONS FAVOURABLE REGIONS IN THE CARBOHYDRATE SURROUNDINGS. 2011.
KOZMON, Stanislav - MATUŠKA, Radek - SPIWOK, Vojtěch - KOČA, Jaroslav.
THEORETICAL STUDY OF THE CARBOHYDRATES DISPERSION INTERACTIONS WITH CONDENSED AROMATIC MOIETIES. 2011.
ALÁN, Jan - DEJMKOVÁ, Eva - KULHÁNEK, Petr - KOČA, Jaroslav - WIMMEROVÁ, Michaela.
Thermodynamics behind CV-IIL binding of saccharides. 2011. ISBN 978-88-900948-8-0.
KOZMON, Stanislav - MATUŠKA, Radek - SPIWOK, Vojtech - KOČA, Jaroslav.
Three-Dimensional Potential Energy Surface of Selected Carbohydrates' CH/p Dispersion Interactions Calculated by High-Level Quantum Mechanical Methods. Chemistry - A European Journal, Weinheim, WILEY-VCH Verlag, Germany. ISSN 0947-6539, 2011, vol. 17, no. 20, pp. 5680-5690.
KULHÁNEK, Petr - ALÁN, Jan - KOČA, Jaroslav.
Virtual screening and in silico design of novel inhibitors of bacterial lectins. 2011.
Virtual screening and in sillico design of novel inhibitors of bacterial lectins. 2011. ISBN 978-80-210-5549-0.
OPPELT, Jan - TICHÝ, Boris - MRÁZ, Marek - SVOBODOVÁ VAŘEKOVÁ, Radka - KOČA, Jaroslav.
Zpracování dat z vysoce výkonných sekvenátorů. 2011.
Computational study of lectin-carbohydrate interactions. 2010. ISBN 978-80-210-5164-5.
STŘELCOVÁ, Zora - KULHÁNEK, Petr - KOČA, Jaroslav.
Computational Study of the MutH Enzyme Reactivity. 2010.
ALÁN, Jan - KULHÁNEK, Petr - KOČA, Jaroslav.
Employment of free energy calculations to estimation of carbohydrates affinities towards PA-IIL superfamily lectins. 2010.
IONESCU, Crina-Maria - SVOBODOVÁ VAŘEKOVÁ, Radka - VANĚK, Jakub - KOČA, Jaroslav.
Fast methods of atomic charge calculation: parameterization of EEM for applicability to metal containing proteins. In 8th Discussions in Structural Molecular Biology. : 2010. 19.3.2010.
IONESCU, Crina-Maria - SVOBODOVÁ VAŘEKOVÁ, Radka - RADĚJ, Tomáš - ONDŘEJ, Skřehota - KOČA, Jaroslav.
Fast methods of atomic charge calculation: parameterization of EEM for applicability to proteins. In 8th European Conference on Computational Chemistry. : 2010. 2010.
Functional studies of Ralstonia solanacearum lectin RS20L. In XIV. Setkání biochemiků a molekulárních biologů. Brno : Masarykova Univerzita, 2010. ISBN 978-80-210-5164-5, p. 50-50. 2010, Brno.
ŠTĚPÁN, Jakub - KULHÁNEK, Petr - KŘÍŽ, Zdeněk - KMUNÍČEK, Jan - KOČA, Jaroslav - MATYSKA, Luděk.
grid-CICADA: Efficient Explorer of Conformational Space of Biomolecular Systems. 2010.
MISHRA, Sushil Kumar - ADAM, Jan - WIMMEROVÁ, Michaela - ABAGYAN, Ruben A. - KOČA, Jaroslav.
In silico mutagenesis and docking study of RSL lectin. 2010.
WIESNER, Jiří - KŘÍŽ, Zdeněk - KUČA, Kamil - JUN, Daniel - KOČA, Jaroslav.
Influence of the Acetylcholinesterase Active Site Protonation on Omega Loop and Active Site Dynamics. Journal of Biomolecular Structure & Dynamics, USA, Adenine Press, USA. ISSN 0739-1102, 2010, vol. 28, no. 3, pp. 393-403.
POKORNÁ, Martina - ADAM, Jan - MRÁZKOVÁ, Jana - IMBERTY, Anne - KOČA, Jaroslav - WIMMEROVÁ, Michaela.
Mutagenesis of Lectin PA-IIL from Pseudomonas aeruginosa as a Tool for Preparation of Lectins with Tune Specificity and Affinity. 2010.
Návrh liečiv metódou molekulového dokovania. In Studentský workshop 2010. Brno : Masarykova Univerzita, 2010. ISBN 978-80-210-5164-5, p. 15-15. 2010, Brno.
WIESNER, Jiří - KŘÍŽ, Zdeněk - KOČA, Jaroslav.
pKa Calculations of Key Ionizable Protein Residues in Acetylcholinesterase. In UF5 - Book of Contributions. Neuveden : Neuveden, 2010. pp. 107-108. 2010, Uppsala, Svedsko.
SKŘEHOTA, Ondřej - SVOBODOVÁ VAŘEKOVÁ, Radka - GEIDL, Stanislav - KUDERA, Michal - SEHNAL, David - IONESCU, Crina-Maria - KOČA, Jaroslav.
QSPR Designer - a program to design and evaluate QSPR models. Case study on pKa prediction. In 6th German Conference on Chemoinformatics. : 2010. 9.3.2010.
STŘELCOVÁ, Zora - KULHÁNEK, Petr - KOČA, Jaroslav.
Reaction Mechanism of MutH Enzyme: Quantum Mechanics/Molecular Mechanics Study. 2010.
MISHRA, Navnit Kumar - KŘÍŽ, Zdeněk - WIMMEROVÁ, Michaela - KOČA, Jaroslav.
Recognition of selected monosaccharides by Pseudomonas aeruginosa Lectin II analyzed by molecular dynamics and free energy calculations. Carbohydrate Research, USA. ISSN 0008-6215, 2010, vol. 345, no. 10, 1432–1441-10 pp.
SVOBODOVÁ VAŘEKOVÁ, Radka - SEHNAL, David - PRAVDA, Lukáš - OPPELT, Jan - KOČA, Jaroslav.
SiteBinder – software tool for superimposing multiple structural motives. In 8th Discussions in Structural Molecular Biology. Nove Hrady : 2010.
FUKAL, Jiří - KULHÁNEK, Petr - FADRNÁ, Eva - KOČA, Jaroslav.
Study of HincII endonuclease by molecular dynamics methods. 2010.
PASULKA, Josef - KOČA, Jaroslav - ŠTEFL, Richard.
The computational view inside the dynamical behavior of the RNA-binding motive. 2010.
WIESNER, Jiří - KOČA, Jaroslav.
THIOREDOXIN AS A MODEL SYSTEM FOR CALCULATIONS OF PROTONATION STATES OF AMINOACIDS. In Struktura a interakce biomolekul. Neuveden : Neuveden, 2010. pp. 15-15. 2010, Brno, Univerzitni Kampus Bohunice.
WIESNER, Jiří - KŘÍŽ, Zdeněk - KUČA, Kamil - JUN, Daniel - KOČA, Jaroslav.
Why acetylcholinesterase reactivators do not work in butyrylcholinesterase. Journal of Enzyme Inhibition and Medicinal Chemistry, UK, Taylor & Francis. ISSN 1475-6366, 2010, vol. 25, no. 3, pp. 318-322.
WIESNER, Jiří - KŘÍŽ, Zdeněk - KOČA, Jaroslav.
ALTERNATIVE ENTRANCES OPENING IN ACETYLCHOLINESTERASE. 2009. ISBN 978-953-95551-3-7.
Analyzing and modelling thermodynamics; the key to lectin engineering. In Cukrblik 2009. Brno : Masarykova Univerzita, 2009. ISBN 978-80-210-4831-7, p. 11-11. 2009, Brno.
KMUNÍČEK, Jan - KOUŘIL, Daniel - MATYSKA, Luděk - STŘELCOVÁ, Zora - KULHÁNEK, Petr - KOČA, Jaroslav - YEN, Eric.
Catch-All Virtual Organizations - Solution for Heterogeneous and Disperse Grid Users Communities. In ISGC 2009 Proceedings. : 2009.
MISHRA, Navnit Kumar - ALÁN, Jan - ADAM, Jan - KŘÍŽ, Zdeněk - WIMMEROVÁ, Michaela - KOČA, Jaroslav.
Computer modeling and simulations on lectins - tricks and reality. In 15th European Carbohydrate Symposium. Vienna : University of Vienna, 2009. p. 41-41. 19.7.2009, Vienna.
ADAM, Jan - KŘÍŽ, Zdeněk - PROKOP, Martin - CHATZIPAVLOU, Thomais - ZOTOS, Petros - KOČA, Jaroslav - WIMMEROVÁ, Michaela.
CRACKING THE LECTIN CODE ; IN SILICO MODELING AND STRUCTURE-FUNCTIONAL STUDY OF PRINCIPLES DRIVING SUGAR PREFERENCE IN PAIIL FAMILY. In FEBS Journal. Oxford : Wiley-Blackwell, 2009. pp. 12-13. 2009, Praha.
Deciphering the lectin code by means of molecular modelling correlated with structure-functional experimental studies. In XIII. Setkání biochemiků a molekulárních biologů. Brno : Masarykova Univerzita, 2009. ISBN 978-80-210-4830-0, p. 3-3. 2009, Brno.
KŘÍŽ, Zdeněk - KRIŠTOFÍKOVÁ, Zdena - KOČA, Jaroslav.
Differences in conformational behavior of amyloid beta in solvent with different ionic strength. In 34th Congress of the Federation-of-European-Biochemical-Societies. Oxford : Wiley-Blackwell, 2009. p. 148-148. 2009, Praha.
KŘÍŽ, Zdeněk - KRIŠTOFÍKOVÁ, Zdena - KOČA, Jaroslav.
Effect of Ionic Strength on Conformational Behavior of Beta Amyloids. A Computational Study. 2009.
NOVOTNÁ JIROUŠKOVÁ, Zuzana - SVOBODOVÁ VAŘEKOVÁ, Radka - VANĚK, Jakub - KOČA, Jaroslav.
Electronegativity Equalization Method - Fast Method For Charge Calculation. 2009.
Free energy calculations on Pseudomonas aeruginosa lectin PA-IIL complexed with various carbohydrates. In Current chemistry and biochemistry of carbohydrates. Vyd. 1st edition. Brno (Czech Republic) : Masarykova univerzita, 2009. ISBN 978-80-210-4831-7, p. 21-21. 16.4.2009, Brno.
STŘELCOVÁ, Zora - KULHÁNEK, Petr - KMUNÍČEK, Jan - KOČA, Jaroslav - MATYSKA, Luděk.
Implementation and Testing of Multiple Walkers Approach Based Free Energy Calculations in the Grid Environment. In GCCP Proceedings. Bratislava, Slovakia : Institute of Informatics SAS, 2009. ISBN 978-80-970145-1-3, pp. 29-36. 26.10.2009, Bratislava, Slovakia.
ŠTĚPÁN, Jakub - KULHÁNEK, Petr - KOČA, Jaroslav - MISHRA, Navnit Kumar.
Implementation of Parallel Analyzes of Molecular Dynamics Simulation Trajectories. 2009.
WIMMEROVÁ, Michaela - MISHRA, Navnit Kumar - POKORNÁ, Martina - KOČA, Jaroslav.
Importance of oligomerisation on Pseudomonas aeruginosa Lectin-II binding affinity. In silico and in vitro mutagenesis. Journal of Molecular Modeling, USA. ISSN 1610-2940, 2009, vol. 15, no. 6, pp. 673-679.
KŘÍŽ, Zdeněk - KRIŠTOFÍKOVÁ, Zdena - KOČA, Jaroslav.
Investigating effect of ionic strength on conformational behavior of beta amyloids. 2009.
STŘELCOVÁ, Zora - KULHÁNEK, Petr - KMUNÍČEK, Jan - KOČA, Jaroslav - MATYSKA, Luděk.
Large-Scale Free Energy Calculations as Showcase of Worldwide Grid Usability. 2009.
Molecular modelling studies of Ralstonia solanacearum lectin RS20L. In Cukrblik 2009. Brno : Masarykova Univerzita, 2009. ISBN 978-80-210-4831-7, p. 23-23. 2009, Brno.
MISHRA, Sushil Kumar - ADAM, Jan - KŘÍŽ, Zdeněk - WIMMEROVÁ, Michaela - KOČA, Jaroslav.
Nature of lectin carbohydrate interactions and how to treat them by computational chemistry tools. In Glycoconjugate Journal, "20th International Symposium on Glycoconjugates Glycans: From Molecules to Structures to Therapeutics, San Juan, Puerto Rico. Netherlands : Springer, 2009. p. 875-876. 2009, San Juan, Puerto Rico.
Revealing the mysteries of the RS20L lectin from Ralstonia solanacearum ; a molecular modelling study. In XIII. Setkání biochemiků a molekulárních biologů. Brno : Masarykova Univerzita, 2009. ISBN 978-80-210-4830-0, p. 109-109. 2009, Brno.
FADRNÁ, Eva - ŠPAČKOVÁ, Naděžda - JOANNA, Sarzynska - KOČA, Jaroslav - OROZCO, Modesto - CHEATHAM, Thomas - KULINSKI, Tadeusz - SPONER, Jiri.
Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields. Journal of Chemical Theory and Computation. ISSN 1549-9618, 2009, vol. 5, no. 9, pp. 2514-2530.
NOVOTNÁ JIROUŠKOVÁ, Zuzana - ABAGYAN, Ruben A. - KOČA, Jaroslav.
Solvation Energy Calculation Based on Electronegativity Equalization Method's (EEM) Charges, Internal Coordinate Mechanics's (ICM) Charges and Charges Based on Partition Coefficients. 2009. ISBN 978-80-7378-098-2.
PASULKA, Josef - KOČA, Jaroslav - ŠTEFL, Richard.
The molecular dynamics study of the RNA-binding domain of ADAR2 bound to dsRNA. 2009.
PROKOP, Martin - ADAM, Jan - KŘÍŽ, Zdeněk - WIMMEROVÁ, Michaela - KOČA, Jaroslav.
TRITON 4 : software for ligand-binding protein engineering. 2009.
MISHRA, Navnit Kumar - KHICHARIYA, Atul - WIMMEROVÁ, Michaela - KOČA, Jaroslav.
A Detailed Analysis of Protein Carbohydrate Interactions by Computational Tools. In 24th International Carbohydrate Symposium. Oslo : ICS, 2008. p. 70-70. 27.7.2008, Oslo, Norway.
KŘÍŽ, Zdeněk - ADAM, Jan - PROKOP, Martin - WIMMEROVÁ, Michaela - KOČA, Jaroslav.
DECIPHERING THE SUGAR PREFERENCE RULES - COMPUTER-ASSISTED PROTEIN ENGINEERING OF BACTERIAL LECTIN PA-IIL. In 33rd FEBS Congress and 11th IUBMB Conference. OXFORD : BLACKWELL PUBLISHING, 2008. p. 1-1. 28.6.2008, Athens.
BÁRTOVÁ, Iveta - KOČA, Jaroslav - OTYEPKA, Michal.
Functional Flexibility of Human Cyclin-Dependent Kinase-2 and Its Evolutionarily Conservation. Protein Science, COLD SPRING HARBOR LAB PRESS. ISSN 0961-8368, 2008, vol. 17, no. 1, pp. 22-33.
ADAM, Jan - POKORNÁ, Martina - KŘÍŽ, Zdeněk - PROKOP, Martin - KOČA, Jaroslav - WIMMEROVÁ, Michaela.
In Silico and In Vitro Mutagenesis of PA-IIL Lectin - Correlation with Structure-Function Analysis. In Proceedings of the Eighth Triennial Congress of the World Association of Theoretical and Computational Chemists (WATOC 2008). Sydney : World Association of Theoretical and Computational Chemists, 2008. ISBN 978-0-646-50151-2, p. 475-475. 2008, Sydney.
ADAM, Jan - KŘÍŽ, Zdeněk - PROKOP, Martin - WIMMEROVÁ, Michaela - KOČA, Jaroslav.
In silico mutagenesis and docking studies of Pseudomonas aeruginosa lectin PA-IIL - predicting binding modes and energies. Journal of Chemical Information and Modeling, USA. ISSN 1549-9596, 2008, vol. 48, no. 11, pp. 2234-2242.
MATOUŠEK, Jiří - ČAJAN, Michal - KULHÁNEK, Petr - KOČA, Jaroslav.
Mechanism of Hydrogen Bond Array Isomerization in Tetrahydroxycalix[4]arene and Tetrahydroxythiacalix[4]arene. Journal of Physical Chemistry A, USA, The American Chemical Society, USA. ISSN 1089-5639, 2008, vol. 112, no. 1, pp. 1076-1084.
PETŘEK, Martin - KOČA, Jaroslav - OTYEPKA, Michal.
MOLE 1.n. 2008.
MISHRA, Navnit Kumar - KULHÁNEK, Petr - ŠNAJDROVÁ, Lenka - PETŘEK, Martin - IMBERTY, Anne - KOČA, Jaroslav.
Molecular dynamics study of Pseudomonas eruginosa lectin-II complexed with monosaccharides. Proteins: Structure, Function, and Bioinformatics, Wiley, USA. ISSN 0887-3585, 2008, vol. 72, no. 1, 382–392-11 pp.
PETŘEK, Martin - KOČA, Jaroslav - OTYEPKA, Michal.
MOLEOnline 1.n. 2008.
ADAM, Jan - KŘÍŽ, Zdeněk - PROKOP, Martin - POKORNÁ, Martina - IMBERTY, Anne - KOČA, Jaroslav - WIMMEROVÁ, Michaela.
Protein engineering of carbohydrate-binding proteins: Calculations and experiment. In Computational Biophysics with Chemical Accuracy. Antigua : RSC, 2008. p. 25-25. 14.1.2008, Antigua.
BÁRTOVÁ, Iveta - KOČA, Jaroslav - OTYEPKA, Michal.
Regulatory Phosphorylations of Cyclin-Dependent Kinase 2: An Insight from the Molecular Dynamics Simulations. Journal of Molecular Modeling, USA. ISSN 1610-2940, 2008, vol. 14, no. 8, pp. 761-768.
JIROUŠKOVÁ, Zuzana - SVOBODOVÁ VAŘEKOVÁ, Radka - VANĚK, Jakub - KOČA, Jaroslav.
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, USA. ISSN 0192-8651, 2008, vol. 2009, no. 30, pp. 1174-1178.
ADAM, Jan - KŘÍŽ, Zdeněk - MALINOVSKÁ, Lenka - LAMEIGNERE, Emily - IMBERTY, Anne - KOČA, Jaroslav - WIMMEROVÁ, Michaela.
Studying the binding properties of BclA lectin - experiment and modeling. In FEBS Journal. OXFORD : BLACKWELL PUBLISHING, 2008. p. 175-175. 2008, Athens.
MISHRA, Navnit Kumar - PETŘEK, Martin - WIMMEROVÁ, Michaela - IMBERTY, Anne - KOČA, Jaroslav.
Theoretical study of the lectin-carbohydrate interactions. In FEBS Journal Volume 275 Supplement 1. Vyd. 2008. Oxford (UK) : Blackwell Publishing Ltd., 2008. p. 459-459. 28.6.2008, Athens, Greece.
PROKOP, Martin - ADAM, Jan - KŘÍŽ, Zdeněk - WIMMEROVÁ, Michaela - KOČA, Jaroslav.
TRITON - Software for In Silico Engineering of Carbohydrate Binding Proteins. In Proceedings of the Eighth Triennial Congress of the World Association of Theoretical and Computational Chemists (WATOC 2008). Sydney : World Association of Theoretical and Computational Chemists, 2008. ISBN 978-0-646-50151-2, p. 035-035. 2008, Sydney.
PROKOP, Martin - ADAM, Jan - KŘÍŽ, Zdeněk - WIMMEROVÁ, Michaela - KOČA, Jaroslav.
TRITON: a graphical tool for ligand-binding protein engineering. Bioinformatics, Oxford University Press, Great Britain. ISSN 1367-4803, 2008, vol. 24, no. 17, pp. 1955-1956.
WIESNER, Jiří - KŘÍŽ, Zdeněk - KUČA, Kamil - JUN, Daniel - KOČA, Jaroslav.
Acetylcholinesterases - the similarities and differences. Journal of Enzyme Inhibition and Medicinal Chemistry, UK, Taylor & Francis. ISSN 1475-6366, 2007, vol. 22, no. 4, pp. 417-424.
WIESNER, Jiří - KŘÍŽ, Zdeněk - KOČA, Jaroslav.
Alternative entrances into the acetylcholinesterase active site. 2007.
ADAM, Jan - POKORNÁ, Martina - KŘÍŽ, Zdeněk - IMBERTY, Anne - SABIN, Charles - KOČA, Jaroslav - WIMMEROVÁ, Michaela.
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