Selected publications

Publications that are part of the Web of Science database, possibly also other publications chosen by authors.

2020

• Varadi, M; Bcrrisford, J; Deshpande, M; Nair, SS; Gutmanas, A; Armstrong, D; Pravda, L; Al-Lazikani, B; Anyango, S; Barton, GJ; Berka, K; Blundell, T; Borkakoti, N; Dana, J; Das, S; Dey, S; Di Micco, P; Fraternali, F; Gibson, T; Helmer-Citterich, M; Hoksza, D; Huang, LC; Jain, R; Jubb, H; Kannas, C; Kannan, N; Koca, J; Krivak, R; Kumar, M; Levy, ED; Madeira, F; Madhusudhan, MS; Martell, HJ; MacGowan, S; McGreig, JE; Mir, S; Mukhopadhyay, A; Parca, L; Paysan-Lafosse, T; Radusky, L; Ribeiro, A; Serrano, L; Sillitoe, I; Singh, G; Skoda, P; Svobodova, R; Tyzack, J; Valencia, A; Fernandez, EV; Vranken, W; Wass, M; Thornton, J; Sternberg, M; Orengo, C; Velankar, S, 2020: PDBe-KB: a community-driven resource for structural and functional annotations. NUCLEIC ACIDS RESEARCH 48(D1), p. D344 - D353, doi: 10.1093/nar/gkz853
• Armstrong, DR; Berrisford, JM; Conroy, MJ; Gutmanas, A; Anyango, S; Choudhary, P; Clark, AR; Dana, JM; Deshpande, M; Dunlop, R; Gane, P; Gaborova, R; Gupta, D; Haslam, P; Koca, J; Mak, L; Mir, S; Mukhopadhyay, A; Nadzirin, N; Nair, S; Paysan-Lafosse, T; Pravda, L; Sehnal, D; Salih, O; Smart, O; Tolchard, J; Varadi, M; Svobodova-Varekova, R; Zaki, H; Kleywegt, GJ; Velankar, S, 2020: PDBe: improved findability of macromolecular structure data in the PDB. NUCLEIC ACIDS RESEARCH 48(D1), p. D335 - D343, doi: 10.1093/nar/gkz990
• Raček, T; Schindler, O; Toušek, D; Horský, V; Berka, K; Koča, J; Svobodová, R , 2020: Atomic Charge Calculator II: web-based tool for the calculation of partial atomic charges.. NUCLEIC ACIDS RESEARCH , doi: 10.1093/nar/gkaa367

2019

• Burley, SK; Berman, HM; Bhikadiya, C; Bi, CX; Chen, L; Di Costanzo, L; Christie, C; Duarte, JM; Dutta, S; Feng, ZK; Ghosh, S; Goodsell, DS; Green, RK; Guranovic, V; Guzenko, D; Hudson, BP; Liang, YH; Lowe, R; Peisach, E; Periskova, I; Randle, C; Rose, A; Sekharan, M; Shao, CH; Tao, YP; Valasatava, Y; Voigt, M; Westbrook, J; Young, J; Zardecki, C; Zhuravleva, M; Kurisu, G; Nakamura, H; Kengaku, Y; Cho, H; Sato, J; Kim, JY; Ikegawa, Y; Nakagawa, A; Yamashita, R; Kudou, T; Bekker, GJ; Suzuki, H; Iwata, T; Yokochi, M; Kobayashi, N; Fujiwara, T; Velankar, S; Kleywegt, GJ; Anyango, S; Armstrong, DR; Berrisford, JM; Conroy, MJ; Dana, JM; Deshpande, M; Gane, P; Gaborova, R; Gupta, D; Gutmanas, A; Koca, J; Mak, L; Mir, S; Mukhopadhyay, A; Nadzirin, N; Nair, S; Patwardhan, A; Paysan-Lafosse, T; Pravda, L; Salih, O; Sehnal, D; Varadi, M; Varekova, R; Markley, JL; Hoch, JC; Romero, PR; Baskaran, K; Maziuk, D; Ulrich, EL; Wedell, JR; Yao, HY; Livny, M; Ioannidis, YE, 2019: Protein Data Bank: the single global archive for 3D macromolecular structure data. NUCLEIC ACIDS RESEARCH 47(D1), p. D520 - D528, doi: 10.1093/nar/gky949

2018

• Varekova, RS; Midlik, A; Varekova, IH; Hutar, J; Navratilova, V; Koca, J; Berka, K, 2018: Secondary Structure Elements - Annotations and Schematic 2D Visualizations Stable for Individual Protein Families. BIOPHYSICAL JOURNAL 114(3), p. 46A - 47A
• Sehnal, D; Deshpande, M; Rose, A; Pravda, L; Midlik, A; Varekova, RS; Mir, S; Berka, K; Velankar, S; Koca, J, 2018: Interactive 3D Macromolecular Structure Data Mining with MolQL and Litemol Suite. BIOPHYSICAL JOURNAL 114(3), p. 47A - 47A, doi: 10.1016/j.bpj.2017.11.308
• Mishra, SK; Koca, J; Yamaguchi, Y, 2018: Binding Free Energy Calculation of Protein-Carbohydrate Complexes: Learnings so Far. BIOPHYSICAL JOURNAL 114(3), p. 57A - 57A, doi: 10.1016/j.bpj.2017.11.365
• Trnka, T; Tvaroska, I; Koca, J, 2018: Automated Training of ReaxFF Reactive Force Fields for Energetics of Enzymatic Reactions. JOURNAL OF CHEMICAL THEORY AND COMPUTATION 14(1), p. 291 - 302, doi: 10.1021/acs.jctc.7b00870
• Mishra, SK; Koca, J, 2018: Assessing the Performance of MM/PBSA, MM/GBSA, and QM-MM/GBSA Approaches on Protein/Carbohydrate Complexes: Effect of Implicit Solvent Models, QM Methods, and Entropic Contributions. JOURNAL OF PHYSICAL CHEMISTRY B 122(34), p. 8113 - 8121, doi: 10.1021/acs.jpcb.8b03655
• Pravda, L; Sehnal, D; Varekova, RS; Navratilova, V; Tousek, D; Berka, K; Otyepka, M; Koca, J, 2018: ChannelsDB: database of biomacromolecular tunnels and pores. NUCLEIC ACIDS RESEARCH 46(D1), p. D399 - D405, doi: 10.1093/nar/gkx868
• Pravda, L; Sehnal, D; Berka, K; Navratilova, V; Tousek, D; Bazgier, V; Varekova, RS; Otyepka, M; Koca, J, 2018: Channelsdb and Moleonline - Database and Tool for Analysis of Biomacromolecular Tunnels and Pores. BIOPHYSICAL JOURNAL 114(3), p. 342A - 343A, doi: 10.1016/j.bpj.2017.11.1912
• Janos, P; Kozmon, S; Tvaroska, I; Koca, J, 2018: How Mycobacterium tuberculosis Galactofuranosyl Transferase2 (GlfT2) Generates Alternating beta-(1-6) and beta-(1-5) Linkages: AQM/MM Molecular Dynamics Study of the Chemical Steps. CHEMISTRY-A EUROPEAN JOURNAL 24(27), p. 7051 - 7059, doi: 10.1002/chem.201800558

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
• 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, doi: 10.1038/nmeth.4499
• 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
• 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
• 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), doi: 10.1371/journal.pone.0189375
• 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, doi: 10.1093/bioinformatics/btx465

2016

• 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, doi: 10.1186/s13321-016-0171-1
• Janos, P; Kozmon, S; Tvaroska, I; Koca, J, 2016: Three-dimensional homologymodel of GlcNAc-TV glycosyltransferase. GLYCOBIOLOGY 26(7), p. 757 - 771, doi: 10.1093/glycob/cww010
• Strelcova, Z; Kulhanek, P; Friak, M; Fabritius, HO; Petrov, M; Neugebauer, J; Koca, J, 2016: The structure and dynamics of chitin nanofibrils in an aqueous environment revealed by molecular dynamics simulations. RSC ADVANCES 6(36), p. 30710 - 30721, doi: 10.1039/c6ra00107f
• Perczel, A; Atanasov, AG; Sklenar, V; Novacek, J; Papouskova, V; Kaderavek, P; Zidek, L; Kozlowski, H; Watly, J; Hecel, A; Kolkowska, P; Koca, J; Svobodova-Varekova, R; Pravda, L; Sehnal, D; Horsky, V; Geidl, S; Enriz, RD; Matejka, P; Jenistova, A; Dendisova, M; Kokaislova, A; Weissig, V; Olsen, M; Coffey, A; Ajuebor, J; Keary, R; Sanz-Gaitero, M; Raaij, MJ; McAuliffe, O; Waltenberger, B; Mocan, A; Smejkal, K; Heis, EH; Diederich, M; Musiol, R; Kosmrlj, J; Polanski, J; Jampilek, J, 2016: The Eighth Central European Conference ´´Chemistry towards Biology´´: Snapshot. MOLECULES 21(10), doi: 10.3390/molecules21101381
• 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, doi: 10.1021/acs.jctc.6b00531

2015

• 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, doi: 10.1093/nar/gku1118
• Estarellas, C; Otyepka, M; Koca, J; Banas, P; Krepl, M; Sponer, J, 2015: Molecular dynamic simulations of protein/RNA complexes: CRISPR/Csy4 endoribonuclease. BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS 1850(5), p. 1072 - 1090, doi: 10.1016/j.bbagen.2014.10.021
• 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), doi: 10.1371/journal.pcbi.1004061
• 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, doi: 10.1186/s13321-015-0099-x
• 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, doi: 10.1021/acs.jctc.5b00159
• 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, doi: 10.1021/ci500758w
• 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, doi: 10.1186/s13321-015-0107-1
• 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, doi: 10.1093/nar/gkv994
• 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, doi: 10.1093/nar/gkv785
• 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, doi: 10.1021/jp511235f

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, doi: 10.1021/ct4009969
• Demo, G; Horska, V; Fliedrova, B; Stepan, J; Koca, J; Weignerova, L; Kren, V; Wimmerova, M, 2014: Protein engineering study of beta-mannosidase to set up a potential chemically efficient biocatalyst. GLYCOBIOLOGY 24(12), p. 1301 - 1311, doi: 10.1093/glycob/cwu074
• Stadlbauer, P; Trantirek, L; Cheatham, TE; Koca, J; Sponer, J, 2014: Triplex intermediates in folding of human telomeric quadruplexes probed by microsecond-scale molecular dynamics simulations. BIOCHIMIE 105, p. 22 - 35, doi: 10.1016/j.biochi.2014.07.009
• 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, doi: 10.1007/s10822-014-9774-7
• Mishra, SK; Kara, M; Zacharias, M; Koca, J, 2014: Enhanced conformational sampling of carbohydrates by Hamiltonian replica-exchange simulation. GLYCOBIOLOGY 24(1), p. 70 - 84, doi: 10.1093/glycob/cwt093
• Pravda, L; Berka, K; Varekova, RS; Sehnal, D; Banas, P; Laskowski, RA; Koca, J; Otyepka, M, 2014: Anatomy of enzyme channels. BMC BIOINFORMATICS 15, doi: 10.1186/s12859-014-0379-x

2013

• 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, doi: 10.1186/1758-2946-5-18
• 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, doi: 10.1186/1758-2946-5-39
• 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, doi: 10.1021/ci400448n
• 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, doi: 10.1093/nar/gkt412
• Emmer, J; Vavrinska, A; Sychrovsky, V; Benda, L; Kriz, Z; Koca, J; Boelens, R; Sklenar, V; Trantirek, L, 2013: Influence of the O-phosphorylation of serine, threonine and tyrosine in proteins on the amidic N-15 chemical shielding anisotropy tensors. JOURNAL OF BIOMOLECULAR NMR 55(1), p. 59 - 70, doi: 10.1007/s10858-012-9686-6
• Krepl, M; Reblova, K; Koca, J; Sponer, J, 2013: Bioinformatics and Molecular Dynamics Simulation Study of L1 Stalk Non-Canonical rRNA Elements: Kink-Turns, Loops, and Tetraloops. JOURNAL OF PHYSICAL CHEMISTRY B 117(18), p. 5540 - 5555, doi: 10.1021/jp401482m
• 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), doi: 10.1371/journal.pone.0062914

2012

• Berka, K; Hanak, O; Sehnal, D; Banas, P; Navratilova, V; Jaiswal, D; Ionescu, CM; Varekova, RS; Koca, J; Otyepka, M, 2012: MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels. NUCLEIC ACIDS RESEARCH 40(W1), p. W222 - W227, doi: 10.1093/nar/gks363
• 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), doi: 10.1371/journal.pone.0046032
• 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, doi: 10.1021/ci200444d
• Krepl, M; Zgarbova, M; Stadlbauer, P; Otyepka, M; Banas, P; Koca, J; Cheatham, TE; Jurecka, P; Sponer, J, 2012: Reference Simulations of Noncanonical Nucleic Acids with Different chi Variants of the AMBER Force Field: Quadruplex DNA, Quadruplex RNA, and Z-DNA. JOURNAL OF CHEMICAL THEORY AND COMPUTATION 8(7), p. 2506 - 2520, doi: 10.1021/ct300275s
• Mishra, SK; Sund, J; Aqvist, J; Koca, J, 2012: Computational prediction of monosaccharide binding free energies to lectins with linear interaction energy models. JOURNAL OF COMPUTATIONAL CHEMISTRY 33(29), p. 2340 - 2350, doi: 10.1002/jcc.23081
• 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
• Soliman, NA; Kulhanek, P; Koca, J, 2012: Influence of stereochemistry on proton transfer in protonated tripeptide models. JOURNAL OF MOLECULAR MODELING 18(3), p. 871 - 879, doi: 10.1007/s00894-011-1116-2
• 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, doi: 10.1021/ci200529n
• 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), doi: 10.1371/journal.pcbi.1002565

2011

• 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, doi: 10.1021/ci200133w
• 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, doi: 10.1002/chem.201002876
• Kozmon, S; Matuska, R; Spiwok, V; Koca, J, 2011: Dispersion interactions of carbohydrates with condensate aromatic moieties: Theoretical study on the CH-pi interaction additive properties. PHYSICAL CHEMISTRY CHEMICAL PHYSICS 13(31), p. 14215 - 14222, doi: 10.1039/c1cp21071h