Prof. Jaroslav Koča

2017

• BERKA, K; SEHNAL, D; BAZGIER, V; PRAVDA, L; SVOBODOVA-VAREKOVA, R; OTYEPKA, M; KOCA, J, 2017:Mole 2.5-Tool for Detection and Analysis of Macromolecular Pores and Channels. BIOPHYSICAL JOURNAL 112 (3), p. 292A - 293A.
• HOUSER, J; KOZMON, S; MISHRA, D; MISHRA, SK; ROMANO, PR; WIMMEROVA, M; KOCA, J, 2017:Influence of Trp flipping on carbohydrate binding in lectins. An example on Aleuria aurantia lectin AAL. PLOS ONE 12 (12)
• PRAVDA, L; SEHNAL, D; VAREKOVA, RS; KOCA, J, 2017:Effective on-Demand Mining of Structural Databases. BIOPHYSICAL JOURNAL 112 (3), p. 348A - 348A.
• RAMOS, RJT; MARTINS, ACD; DELGADO, GD; IONESCU, CM; URMENYI, TP; SILVA, R; KOCA, J, 2017:CrocoBLAST: Running BLAST efficiently in the age of next-generation sequencing. BIOINFORMATICS 33 (22), p. 3648 - 3651.
• SEHNAL, D; DESHPANDE, M; VAREKOVA, RS; MIR, S; BERKA, K; MIDLIK, A; PRAVDA, L; VELANKAR, S; KOCA, J, 2017:LiteMol suite: interactive web-based visualization of large-scale macromolecular structure data. NATURE METHODS 14 (12), p. 1121 - 1122.
• SEHNAL, D; DESHPANDE, M; VAREKOVA, RS; MIR, S; BERKA, K; MIDLIK, A; PRAVDA, L; VELANKAR, S; KOCA, J, 2017:Real-Time Interactive Visualisation of Large Macromolecular Assemblies and Molecular Machines at Atomic Resolution. BIOPHYSICAL JOURNAL 112 (3), p. 178A - 178A.
• VAREKOVA, RS; HORSKY, V; SEHNAL, D; BENDOVA, V; PRAVDA, L; KOCA, J, 2017:Quo Vadis, Biomacromolecular Structure Quality. BIOPHYSICAL JOURNAL 112 (3), p. 346A - 347A.

2016

• JANOS, P; TRNKA, T; KOZMON, S; TVAROSKA, I; KOCA, J, 2016:Different QM/MM Approaches To Elucidate Enzymatic Reactions: Case Study on ppGalNAcT2. JOURNAL OF CHEMICAL THEORY AND COMPUTATION 12 (12), p. 6062 - 6076.
• RACEK, T; PAZURIKOVA, J; VAREKOVA, RS; GEIDL, S; KRENEK, A; FALGINELLA, FL; HORSKY, V; HEJRET, V; KOCA, J, 2016:NEEMP: software for validation, accurate calculation and fast parameterization of EEM charges. JOURNAL OF CHEMINFORMATICS 8

2015

• GEIDL, S; BOUCHAL, T; RAČEK, T; SVOBODOVA VAREKOVA, R; HEJRET, V; KŘENEK, A; ABAGYAN, R; KOČA, J, 2015:High-quality and universal empirical atomic charges for chemoinformatics applications. JOURNAL OF CHEMINFORMATICS 7
• GEIDL, S; VAREKOVA, RS; BENDOVA, V; PETRUSEK, L; IONESCU, CM; JURKA, Z; ABAGYAN, R; KOCA, J, 2015:How Does the Methodology of 3D Structure Preparation Influence the Quality of pK(a) Prediction?. JOURNAL OF CHEMICAL INFORMATION AND MODELING 55 (6), p. 1088 - 1097.
• IONESCU, CM; SEHNAL, D; FALGINELLA, FL; PANT, P; PRAVDA, L; BOUCHAL, T; VAREKOVA, RS; GEIDL, S; KOCA, J, 2015:AtomicChargeCalculator: interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules. JOURNAL OF CHEMINFORMATICS 7
• ISLAM, B; STADLBAUER, P; KREPL, M; KOCA, J; NEIDLE, S; HAIDER, S; SPONER, J, 2015:Extended molecular dynamics of a c-kit promoter quadruplex. NUCLEIC ACIDS RESEARCH 43 (18), p. 8673 - 8693.
• KUMARI, M; KOZMON, S; KUHANEK, P; STEPAN, J; TVAROSKA, I; KOCA, J, 2015:Exploring Reaction Pathways for O-GlcNAc Transferase Catalysis. A String Method Study. JOURNAL OF PHYSICAL CHEMISTRY B 119 (12), p. 4371 - 4381.
• MISHRA, SK; CALABRO, G; LOEFFLER, HH; MICHEL, J; KOCA, J, 2015:Evaluation of Selected Classical Force Fields for Alchemical Binding Free Energy Calculations of Protein-Carbohydrate Complexes. JOURNAL OF CHEMICAL THEORY AND COMPUTATION 11 (7), p. 3333 - 3345.
• SEHNAL, D; VAREKOVA, RS; PRAVDA, L; IONESCU, CM; GEIDL, S; HORSKY, V; JAISWAL, D; WIMMEROVA, M; KOCA, J, 2015:ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank. NUCLEIC ACIDS RESEARCH 43 (D1), p. D369 - D375.
• STADLBAUER, P; KUHROVA, P; BANAS, P; KOCA, J; BUSSI, G; TRANTIREK, L; OTYEPKA, M; SPONER, J, 2015:Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations. NUCLEIC ACIDS RESEARCH 43 (20), p. 9626 - 9644.
• TRNKA, T; KOZMON, S; TVAROSKA, I; KOCA, J, 2015:Stepwise Catalytic Mechanism via Short-Lived Intermediate Inferred from Combined QM/MM MERP and PES Calculations on Retaining Glycosyltransferase ppGalNAcT2. PLOS COMPUTATIONAL BIOLOGY 11 (4)

2014

• GKIONIS, K; KRUSE, H; PLATTS, JA; MLADEK, A; KOCA, J; SPONER, J, 2014:Ion Binding to Quadruplex DNA Stems. Comparison of MM and QM Descriptions Reveals Sizable Polarization Effects Not Included in Contemporary Simulations. JOURNAL OF CHEMICAL THEORY AND COMPUTATION 10 (3), p. 1326 - 1340.
• KRIZ, Z; ADAM, J; MRAZKOVA, J; ZOTOS, P; CHATZIPAVLOU, T; WIMMEROVA, M; KOCA, J, 2014:Engineering the Pseudomonas aeruginosa II lectin: designing mutants with changed affinity and specificity. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN 28 (9), p. 951 - 960.

2013

• IONESCU, CM; GEIDL, S; VAREKOVA, RS; KOCA, J, 2013:Rapid Calculation of Accurate Atomic Charges for Proteins via the Electronegativity Equalization Method. JOURNAL OF CHEMICAL INFORMATION AND MODELING 53 (10), p. 2548 - 2558.
• KRIZ, Z; KLUSAK, J; KRISTOFIKOVA, Z; KOCA, J, 2013:How Ionic Strength Affects the Conformational Behavior of Human and Rat Beta Amyloids - A Computational Study. PLOS ONE 8 (5)
• SEHNAL, D; VAREKOVAA, RS; BERKA, K; PRAVDA, L; NAVRATILOVA, V; BANAS, P; IONESCU, CM; OTYEPKA, M; KOCA, J, 2013:MOLE 2.0: advanced approach for analysis of biomacromolecular channels. JOURNAL OF CHEMINFORMATICS 5
• STADLBAUER, P; KREPL, M; CHEATHAM, TE; KOCA, J; SPONER, J, 2013:Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations. NUCLEIC ACIDS RESEARCH 41 (14), p. 7128 - 7143.
• VAREKOVA, RS; GEIDL, S; IONESCU, CM; SKREHOTA, O; BOUCHAL, T; SEHNAL, D; ABAGYAN, R; KOCA, J, 2013:Predicting pK(a) values from EEM atomic charges. JOURNAL OF CHEMINFORMATICS 5

2012

• IONESCU, CM; VAREKOVA, RS; PREHN, JHM; HUBER, HJ; KOCA, J, 2012:Charge Profile Analysis Reveals That Activation of Pro-apoptotic Regulators Bax and Bak Relies on Charge Transfer Mediated Allosteric Regulation. PLOS COMPUTATIONAL BIOLOGY 8 (6)
• KRISTOFIKOVA, Z; KRIZ, Z; RIPOVA, D; KOCA, J, 2012:Interactions of Amyloid beta Peptide 1-40 and Cerebrosterol. NEUROCHEMICAL RESEARCH 37 (3), p. 604 - 613.
• MISHRA, S; ADAMOVA, L; ADAM, J; WIMMEROVA, M; KOCA, J, 2012:Comparison of Docking Software to Predict Saccharide Binding to Proteins Combination with In silico Protein Engineering. GLYCOBIOLOGY 22 (11), p. 1648 - 1649.
• MISHRA, SK; ADAM, J; WIMMEROVA, M; KOCA, J, 2012:In Silico Mutagenesis and Docking Study of Ralstonia solanacearum RSL Lectin: Performance of Docking Software To Predict Saccharide Binding. JOURNAL OF CHEMICAL INFORMATION AND MODELING 52 (5), p. 1250 - 1261.
• SEHNAL, D; VAREKOVA, RS; HUBER, HJ; GEIDL, S; IONESCU, CM; WIMMEROVA, M; KOCA, J, 2012:SiteBinder: An Improved Approach for Comparing Multiple Protein Structural Motifs. JOURNAL OF CHEMICAL INFORMATION AND MODELING 52 (2), p. 343 - 359.
• WIMMEROVA, M; KOZMON, S; NECASOVA, I; MISHRA, SK; KOMAREK, J; KOCA, J, 2012:Stacking Interactions between Carbohydrate and Protein Quantified by Combination of Theoretical and Experimental Methods. PLOS ONE 7 (10)

2011

• KOZMON, S; MATUSKA, R; SPIWOK, V; KOCA, J, 2011:Three-Dimensional Potential Energy Surface of Selected Carbohydrates' CH/pi Dispersion Interactions Calculated by High-Level Quantum Mechanical Methods. CHEMISTRY-A EUROPEAN JOURNAL 17 (20), p. 5680 - 5690.
• VAREKOVA, RS; GEIDL, S; IONESCU, CM; SKREHOTA, O; KUDERA, M; SEHNAL, D; BOUCHAL, T; ABAGYAN, R; HUBER, HJ; KOCA, J, 2011: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 51 (8), p. 1795 - 1806.

2010

• MISHRA, NK; KRIZ, Z; WIMMEROVA, M; KOCA, J, 2010:Recognition of selected monosaccharides by Pseudomonas aeruginosa Lectin II analyzed by molecular dynamics and free energy calculations. CARBOHYDRATE RESEARCH 345 (10), p. 1432 - 1441.

2009

• WIMMEROVA, M; MISHRA, NK; POKORNA, M; KOCA, J, 2009:Importance of oligomerisation on Pseudomonas aeruginosa Lectin-II binding affinity. In silico and in vitro mutagenesis. JOURNAL OF MOLECULAR MODELING 15 (6), p. 673 - 679.

Office 1:

Masarykova univerzita - Centrální řídící struktura Kamenice 753/5, Brno, 625 00, office bud. A4/119