Contact
Email: | |
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Phone: | +420 54949 4947, +420 54949 2685, +420 54949 2685 |
Research group: | Computational Chemistry - Jaroslav Koča |
Department: | Central management structure |
Workplace: |
12. July 2019
Visit of Uteerat Chareontoh, Ambassador of the Kingdom of Thailand at CEITEC BUT
CEITEC Brno University of Technology visited Her Excellency Uteerat Chareontoh to discuss with our institute the possibility of working with…
5. Oct. 2018
New path to more gentle tuberculosis treatment
Researchers at CEITEC MU have defined a new goal for those looking for new ways to fight tuberculosis. Their research makes it possible to…
29. Jan. 2018
Interview with Jaroslav Koča about Czech Science Foundation
Perhaps not everyone knows that apart from the function of scientific director at CEITEC you have also a very important position within the Czech…
19. Dec. 2017
A new CEITEC MU software provides a breakthrough in working with biological databases
Press release, Brno, December 19, 2017 A new software application that works as a virtual microscope for molecules and molecular complexes was…
2. Jan. 2017
Shared Technologies and Instrumentation as a Way to Joint Success / CEITEC MU and Vienna Research Centres Offer Joint Services
The catalogue of services that will be jointly offered to corporations and academic institutions will be compiled by CEITEC Masaryk University in…
Publications that are part of the Web of Science database, possibly also other publications chosen by authors.
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
- Zufanova, Z; Houser, J; Kozmon, S; Mishra, D; Wimmerova, M; Koca, J, 2018: Importance of CH-pi stacking interaction in carbohydrate-protein complexes. FEBS OPEN BIO 8, p. 385 - 385
- 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
- Stepan, J; Kabelka, I; Koca, J; Kulhanek, P, 2018: Behavior of BsoBI endonuclease in the presence and absence of DNA. JOURNAL OF MOLECULAR MODELING 24(1), doi: 10.1007/s00894-017-3557-8
- 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; Toušek, D; Navrátilová, V; Bazgier, V; Berka, K; Svobodová Vareková, R; Koca, J; Otyepka, M, 2018: MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update). NUCLEIC ACIDS RESEARCH , doi: 10.1093/nar/gky309
- Janoš, P; Kozmon, S; Tvaroška, I; Koča, J, 2018: How Mycobacterium tuberculosis Galactofuranosyl Transferase 2 (GlfT2) Generates Alternating β-(1-6) and β-(1-5) Linkages: A QM/MM Molecular Dynamics Study of the Chemical Steps. CHEMISTRY-A EUROPEAN JOURNAL , doi: 10.1002/chem.201800558
- 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
- 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
- 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
- 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, 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
- 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
2017
- 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
- 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
- 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
- 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
- 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
- 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
2015
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
2014
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
2012
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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, doi: 10.1007/s11064-011-0650-8
- 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
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, doi: 10.1002/chem.201002876
- 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: 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
2010
- Wiesner, J; Kriz, Z; Kuca, K; Jun, D; Koca, J, 2010: Why acetylcholinesterase reactivators do not work in butyrylcholinesterase. JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY 25(3), p. 318 - 322, doi: 10.3109/14756360903179427
- Wiesner, J; Kriz, Z; Kuca, K; Jun, D; Koca, J, 2010: Influence of the Acetylcholinesterase Active Site Protonation on Omega Loop and Active Site Dynamics. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS 28(3), p. 393 - 403
- 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, doi: 10.1016/j.carres.2010.04.021
2009
- Fadrna, E; Spackova, N; Sarzynska, J; Koca, J; Orozco, M; Cheatham, TE; Kulinski, T; Sponer, J, 2009: Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields. JOURNAL OF CHEMICAL THEORY AND COMPUTATION 5(9), p. 2514 - 2530
- 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
- Czech National Infrastructure for Biological Data (LM2015047), Ministerstvo školství, mládeže a tělovýchovy ČR, 2016 - 2019
- ELIXIR-EXCELERATE: Fast-track ELIXIR implementation and drive early user exploitation across the life-sciences (676559), Evropská unie, 2015 - 2019
- The ERA Chair Culture as a Catalyst to Maximize the Potential of CEITEC, Evropská unie, 2014 - 2019
- BISON - BrIdging Structural BiOlogy with Biological SyNthesis and Self Assembly to Reveal Key Processes in Living Systems (692068), Evropská unie, 2016 - 2018
- Podpora realizace a koordinace ukončování a udržitelnosti projektů operačních programů, příprava na nové programovací období, Ministerstvo školství, mládeže a tělovýchovy ČR, 2015 - 2015
- CEITEC - Central European Institute of Technology (CZ.1.05/1.1.00/02.0068), Ministerstvo školství, mládeže a tělovýchovy ČR, 2011 - 2015
- Zaměstnáním nejlepších mladých vědců k rozvoji mezinárodní spolupráce (CZ.1.07/2.3.00/30.0037), Ministerstvo školství, mládeže a tělovýchovy ČR, 2013 - 2015
- Zaměstnáním čerstvých absolventů doktorského studia k vědecké excelenci (CZ.1.07/2.3.00/30.0009), Ministerstvo školství, mládeže a tělovýchovy ČR, 2012 - 2015
- SYLICA - Synergies of Life and Material Sciences to Create a New Future (286154), Evropská unie, 2011 - 2015
- InterBioNet - Podpora mezinárodní a mezisektorové spolupráce ve výzkumu a vývoji v oblasti věd o živé přírodě (CZ.1.07/2.4.00/17.0042), Ministerstvo školství, mládeže a tělovýchovy ČR, 2011 - 2014
- Podpora realizace a koordinace ukončování a udržitelnosti projektů operačních programů (ROZV/11/2013), Ministerstvo školství, mládeže a tělovýchovy ČR, 2013 - 2013
- REAKTIVACE - Výzkum reaktivace acetylcholinesterasy metodami výpočetní chemie (OVMASUN200901), Ministerstvo obrany ČR, 2009 - 2012
- Molekulární a strukturní biologie vybraných cytostatik. Od mechanických studií k chemoterapii rakoviny (GD301/09/H004), Grantová agentura ČR, 2009 - 2012
- Testování vazby mezi cerebrosterolem a peptidem amyloidu beta 1-40 (GA305/09/0457), Grantová agentura ČR, 2009 - 2011
- Program developing interdisciplinary research POtential for the STudies of BIOMolecular INteractions (205872), Evropská unie, 2008 - 2011