Selected publications

2019

• Sehnal, D; Grant, OC, 2019: Rapidly Display Glycan Symbols in 3D Structures: 3D-SNFG in LiteMol. JOURNAL OF PROTEOME RESEARCH 18(2), p. 770 - 774, doi: 10.1021/acs.jproteome.8b00473
• Harnos, J; Canizal, MCA; Jurasek, M; Kumar, J; Holler, C; Schambony, A; Hanakova, K; Bernatik, O; Zdrahal, Z; Gomoryova, K; Gybel, T; Radaszkiewicz, TW; Kravec, M; Trantirek, L; Rynes, J; Dave, Z; Fernandez-Llamazares, AI; Vacha, R; Tripsianes, K; Hoffmann, C; Bryja, V, 2019: Dishevelled-3 conformation dynamics analyzed by FRET-based biosensors reveals a key role of casein kinase 1. NATURE COMMUNICATIONS 10, doi: 10.1038/s41467-019-09651-7
• Buchta, D; Füzik, T; Hrebík, D; Levdansky, Y; Sukeník, L; Mukhamedova, L; Moravcová, J; Vácha, R; Plevka, P., 2019: Enterovirus particles expel capsid pentamers to enable genome release. NATURE COMMUNICATIONS , doi: 10.1038/s41467-019-09132-x

2018

• 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
• 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
• 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
• Tubiana, L; Jurasek, M; Coluzza, I, 2018: Implementing efficient concerted rotations using Mathematica and C code. EUROPEAN PHYSICAL JOURNAL E 41(7), doi: 10.1140/epje/i2018-11694-7
• Grillova, L; Giacani, L; Mikalova, L; Strouhal, M; Strnadel, R; Marra, C; Centurion-Lara, A; Poveda, L; Russo, G; Cejkova, D; Vasku, V; Oppelt, J; Smajs, D, 2018: Sequencing of Treponema pallidum subsp pallidum from isolate UZ1974 using Anti-Treponemal Antibodies Enrichment: First complete whole genome sequence obtained directly from human clinical material. PLOS ONE 13(8), doi: 10.1371/journal.pone.0202619
• 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
• Leber, R; Pachler, M; Kabelka, I; Svoboda, I; Enkoller, D; Vacha, R; Lohner, K; Pabst, G, 2018: Synergism of Antimicrobial Frog Peptides Couples to Membrane Intrinsic Curvature Strain. BIOPHYSICAL JOURNAL 114(8), p. 1945 - 1954, doi: 10.1016/j.bpj.2018.03.006
• 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
• Kabelka, I; Brozek, R; Vacha, R, 2018: Multivalent Inhibitors Preventing Uptake of Virus-Like Particles. BIOPHYSICAL JOURNAL 114(3), p. 279A - 279A, doi: 10.1016/j.bpj.2017.11.1607
• Rose, AS; Sehnal, D; Bliven, S; Burley, SK; Velankar, S, 2018: Molql: Towards a Common General Purpose Molecular Query Language. BIOPHYSICAL JOURNAL 114(3), p. 342A - 342A
• Moturu, TR; Thula, S; Singh, RK; Nodzynski, T; Varekova, RS; Friml, J; Simon, S, 2018: Molecular evolution and diversification of the SMXL gene family. JOURNAL OF EXPERIMENTAL BOTANY 69(9), p. 2367 - 2378, doi: 10.1093/jxb/ery097
• Strouhal, M; Oppelt, J; Mikalova, L; Arora, N; Nieselt, K; González-Candelas F; Šmajs, D, 2018: Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes.. BMC RESEARCH NOTES 11(16), doi: doi: 10.1186/s13104-017-3106-7
• Strouhal, M; Mikalova, L; Haviernik, J; Knauf, S; Bruisten, S; Noordhoek, GT; Oppelt, J; Cejkova, D; Smajs, D, 2018: Complete genome sequences of two strains of Treponema pallidum subsp pertenue from Indonesia: Modular structure of several treponemal genes. PLOS NEGLECTED TROPICAL DISEASES 12(10), doi: 10.1371/journal.pntd.0006867
• Vacha, R; Kabelka, I; Brozek, R, 2018: Translocation of amphiphilic peptides across phospholipid membranes. FEBS OPEN BIO 8, p. 25 - 25
• Pavlasova, G; Borsky, M; Svobodova, V; Oppelt, J; Cerna, K; Novotna, J; Seda, V; Fojtova, M; Fajkus, J; Brychtova, Y; Doubek, M; Pospisilova, S; Mayer, J; Mraz, M, 2018: Rituximab primarily targets an intra-clonal BCR signaling proficient CLL subpopulation characterized by high CD20 levels. LEUKEMIA 32(9), p. 2028 - 2031, doi: 10.1038/s41375-018-0211-0
• Kabelka, I; Vacha, R, 2018: Optimal Hydrophobicity and Reorientation of Amphiphilic Peptides Translocating through Membrane. BIOPHYSICAL JOURNAL 115(6), p. 1045 - 1054, doi: 10.1016/j.bpj.2018.08.012
• Musilova, K; Devan, J; Cerna, K; Seda, V; Pavlasova, G; Sharma, S; Oppelt, J; Pytlik, R; Prochazka, V; Prouzova, Z; Trbusek, M; Zlamalikova, L; Liskova, K; Kruzova, L; Jarosova, M; Mareckova, A; Kornauth, C; Simonitsch-Klupp, I; Schiefer, A; Merkel, O; Mocikova, H; Burda, P; Polakova, K; Kren, L; Mayer, J; Zent, CS; Trneny, M; Evans, A; Janikova, A; Mraz, M, 2018: miR-150 downregulation contributes to the high-grade transformation of follicular lymphoma by upregulating FOXP1 levels. BLOOD
• Cerna, K; Oppelt, J; Musilova, K; Seda, V;Pavlasova, K; Radova, L; Arigoni, M; Calogero, RA; Benes, V; Tbusek, M; Brychtova, Y; Doubek, M; Mayer, J; Pospisilova, S; Mraz, M, 2018: MicroRNA miR-34a downregulates FOXP1 during DNA damage response to limit BCR signalling in chronic lymphocytic leukaemia B cells. LEUKEMIA
• Bartas, M; Cerven, J; Oppelt, J; Peteja, M; Vavra, P; Zonca, P; Prochazka, V; Brazda, V; Pecinka, P, 2018: Liver regeneration during the associating liver partition and portal vein ligation for staged hepatectomy procedure in Sus scrofa is positively modulated by stem cells. ONCOLOGY LETTERS 15(5), p. 6309 - 6321, doi: 10.3892/ol.2018.8108
• 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
• Sandor, R; Slanina, J; Midlik, A; Sebrlova, K; Novotna, L; Carnecka, M; Slaninova, I; Taborsky, P; Taborska, E; Pes, O, 2018: Sanguinarine is reduced by NADH through a covalent adduct. PHYTOCHEMISTRY 145, p. 77 - 84, doi: 10.1016/j.phytochem.2017.10.010
• Mir, S; Alhroub, Y; Anyango, S; Armstrong, DR; Berrisford, JM; Clark, AR; Conroy, MJ; Dana, JM; Deshpande, M; Gupta, D; Gutmanas, A; Haslam, P; Mak, L; Mukhopadhyay, A; Nadzirin, N; Paysan-Lafosse, T; Sehnal, D; Sen, S; Smart, OS; Varadi, M; Kleywegt, GJ; Velankar, S, 2018: PDBe: towards reusable data delivery infrastructure at protein data bank in Europe. NUCLEIC ACIDS RESEARCH 46(D1), p. D486 - D492, doi: 10.1093/nar/gkx1070
• Smetana, J; Oppelt, J; Stork, M; Pour, L; Kuglik, P, 2018: Chromothripsis 18 in multiple myeloma patient with rapid extramedullary relapse. MOLECULAR CYTOGENETICS 11, doi: 10.1186/s13039-018-0357-5
• 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
• 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
• Smart, OS; Horsky, V; Gore, S; Varekova, RS; Bendova, V; Kleywegt, GJ; Velankar, S, 2018: Worldwide Protein Data Bank validation information: usage and trends. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 74, p. 237 - 244, doi: 10.1107/S2059798318003303
• Smart, OS; Horsky, V; Gore, S; Varekova, RS; Bendova, V; Kleywegt, GJ; Velankar, S, 2018: Validation of ligands in macromolecular structures determined by X-ray crystallography. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 74, p. 228 - 236, doi: 10.1107/S2059798318002541
• 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
• Laskowski, RA; Jablonska, J; Pravda, L; Varekova, RS; Thornton, JM, 2018: PDBsum: Structural summaries of PDB entries. PROTEIN SCIENCE 27(1), p. 129 - 134, doi: 10.1002/pro.3289

2017

• Wayhelova, M; Oppelt, J; Smetana, J; Filkova, H; Hladikova, E; Soukalova, J; Gaillyova, R; Kuglik, P, 2017: Two Distinct De novo Pathogenic Sequence Variants in the SCN2A Gene in Children with Early Infantile Epileptic Encephalopathy/Ohtahara Syndrome. JOURNAL OF NEUROLOGICAL DISORDERS 5(6), doi: 10.4172/2329-6895.1000369
• Slany, M; Oppelt, J; Cincarova, L, 2017: Formation of Staphylococcus aureus Biofilm in the Presence of Sublethal Concentrations of Disinfectants Studied via a Transcriptomic Analysis Using Transcriptome Sequencing (RNA-seq).. APPLIED AND ENVIRONMENTAL MICROBIOLOGY 83(24), doi: doi: 10.1128/AEM.01643-17
• Mraz, M; Cerna, K; Oppelt, J; Seda, V; Musilova, K; Pavlasova, G; Mayer, J; Pospisilova, S, 2017: MicroRNA induced by DNA damage response regulates the expression of FOXP1 and therapy response in CLL. LEUKEMIA & LYMPHOMA 58, p. 73 - 74
• 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
• Mikalova, L; Strouhal, M; Oppelt, J; Grange, PA; Janier, M; Benhaddou, N; Dupin, N; Smajs, D, 2017: Human Treponema pallidum 11q/j isolate belongs to subsp endemicum but contains two loci with a sequence in TP0548 and TP0488 similar to subsp pertenue and subsp pallidum, respectively. PLOS NEGLECTED TROPICAL DISEASES 11(3), doi: 10.1371/journal.pntd.0005434
• Fiala, T; Ludvikova, L; Heger, D; Svec, J; Slanina, T; Vetrakova, L; Babiak, M; Necas, M; Kulhanek, P; Klan, P; Sindelar, V, 2017: Bambusuril as a One-Electron Donor for Photoinduced Electron Transfer to Methyl Viologen in Mixed Crystals. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 139(7), p. 2597 - 2603, doi: 10.1021/jacs.6b08589
• Jurasek, M; Vacha, R, 2017: Self-assembled clusters of patchy rod-like molecules. SOFT MATTER 13(41), p. 7492 - 7497, doi: 10.1039/c7sm01384a
• Ruzicka, M; Kulhanek, P; Radova, L; Cechova, A; Spackova, N; Fajkusova, L; Reblova, K, 2017: DNA mutation motifs in the genes associated with inherited diseases. PLOS ONE 12(8), doi: 10.1371/journal.pone.0182377
• 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
• Kabelka, I; Vacha, R, 2017: Peptide features determining its ability of translocation and membrane pore formation. EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS 46, p. S386 - S386
• 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
• 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
• 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

• Molina-Serrano, D; Schiza, V; Demosthenous, C; Stavrou, E; Oppelt, J; Kyriakou, D; Liu, W; Zisser, G; Bergler, H; Dang, WW; Kirmizis, A, 2016: Loss of Nat4 and its associated histone H4 N-terminal acetylation mediates calorie restriction-induced longevity. EMBO REPORTS 17(12), p. 1829 - 1843, doi: 10.15252/embr.201642540
• Smetana, J; Kuglik, P; Greslikova, H; Kupska, R; Nemec, P; Mikulasova, A; Valaskova, I; Oppelt, J; Almasi, M; Krejci, M; Adam, Z; Pour, L; Hajek, R, 2016: Clonal cytogenetics changes in progression of multiple myeloma to extramedullary relapse and plasmocellular leukemia: a case report. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 9(1), p. 49 - +
• Ustrnul, L; Babiak, M; Kulhanek, P; Sindelar, V, 2016: A Cucurbituril Derivative That Exhibits Cation-Modulated Self Assembly. JOURNAL OF ORGANIC CHEMISTRY 81(14), p. 6075 - 6080, doi: 10.1021/acs.joc.6b01288
• Sima, M; Novotny, M; Pravda, L; Sumova, P; Rohousova, I; Volf, P, 2016: The Diversity of Yellow-Related Proteins in Sand Flies (Diptera: Psychodidae). PLOS ONE 11(11), doi: 10.1371/journal.pone.0166191
• Ison, J; Rapacki, K; Menager, H; Kalas, M; Rydza, E; Chmura, P; Anthon, C; Beard, N; Berka, K; Bolser, D; Booth, T Bretaudeau, A; Brezovsky, J; Casadio, R; Cesareni, G; Copens, F; Cornell, M Cuccuru, G; Davidsen, K; Della Vedova, G; Dogan, T; Doppelt-Azeroual, O; Emery, L; Gasteiger, E; Gatter, T; Goldberg, T; Grosjean, M; Gruning, B; Helmer-Citterich, M; Ienasescu, H; Ioannidis, V; Jespersen, MC; Jimenz, R; Juty, N; Juvan, P; Koch, M; Laibe, C; Li, JW; Licata, L; Mareuil, F; Micetic, I; Friborg, RM; Moretti, S; Morris, C; Moller, S; Nenadic, A; Peterson, H; Profiti, G; Rice, P; Romano, P; Roncaglia, P; Saidi, R; Schafferhans, A; Schwammle, V; Smith, C; Sperotto, MM; Stockinger, H; Varekova, RS; Tosatto, SCE; de la Torre, V; Uva, P; Via, A; Yachdav, G; Zambelli, F; Vriend, G; Rost, B; Parkinson, H; Longreen, P; Brunak, S , 2016: Tools and data services registry: a community effort to document bioinformatics resources. NUCLEIC ACIDS RESEARCH 44(D1), doi: 10.1093/nar/gkv1116
• Adams, P; Aertgeerts, K; Bauer, C; Bell, JA; Berman, HM; Bhat, TN; Blaney, JM; Bolton, E; Bricogne, G; Brown, D; Burley, SK; Case, DA; Clark, KL; Darden, T; Emsley, P; Feher, VA; Feng, ZK; Groom, CR; Harris, SF; Hendle, J; Holder, T; Joachimiak, A; Kleywegt, GJ; Krojer, T; Marcotrigiano, J; Mark, AE; Markley, JL; Miller, M; Minor, W; Montelion, GT; Murshudov, G; Nakagawa, A; Nakamura, H; Nicholls, A; Nicklaus, M; Nolte, RT; Padyana, AK; Peishoff, CE; Pieniazek, S; Read, RJ; Shao, CH; Sheriff, S; Smart, O; Soisson, S; Spurlino, J; Stouch, T; Svobodova, R; Tempel, W; Terwilliger, TC; Tronrud, D; Velankar, S; Ward, SC; Warren, GL; Westbrook, JD; Williams, P; Yang, HW; Young, J, 2016: Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop. STRUCTURE 24(4), doi: 10.1016/j.str.2016.02.017
• 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
• Branna, P; Cernochova, J; Rouchal, M; Kulhanek, P; Babinsky, M; Marek, R; Necas, M; Kuritka, I; Vicha, R, 2016: Cooperative Binding of Cucurbit[n]urils and beta-Cyclodextrin to Heteroditopic Imidazolium-Based Guests. JOURNAL OF ORGANIC CHEMISTRY 81(20), p. 9595 - 9604, doi: 10.1021/acs.joc.6b01564
• 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
• Amaro, M; Sachl, R; Aydogan, G; Mikhalyov, I; Vacha, R; Hof, M, 2016: The role of ganglioside GM1 and sphingomyelin in the oligomerisation of beta-amyloid at physiological conditions: a single molecule study. FEBS JOURNAL 283, p. 71 - 71
• Mikulasek, K; Jaron, KS; Kulhanek, P; Bittova, M; Havlis, J, 2016: Sequence-dependent separation of trinucleotides by ion-interaction reversed-phase liquid chromatography A structure-retention study assisted by soft-modelling and molecular dynamics. JOURNAL OF CHROMATOGRAPHY A 1469, p. 88 - 95, doi: 10.1016/j.chroma.2016.09.060
• Phulwale, BV; Mishra, SK; Necas, M; Mazal, C, 2016: Phenanthrylene-butadiynylene and Phenanthrylene-thienylene Macrocycles: Synthesis, Structure, and Properties. JOURNAL OF ORGANIC CHEMISTRY 81(15), p. 6244 - 6252, doi: 10.1021/acs.joc.6b00814
• 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; 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; Pravda, L; Varekova, RS; Ionescu, CM; Koca, J, 2015: PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank. NUCLEIC ACIDS RESEARCH 43(W1), p. W383 - W388, doi: 10.1093/nar/gkv561
• Ihnatova, I; Budinska, E, 2015: ToPASeq: an R package for topology-based pathway analysis of microarray and RNA-Seq data. BMC BIOINFORMATICS 16, doi: 10.1186/s12859-015-0763-1
• KABELKA, I; VACHA, R, 2015: Optimal conditions for opening of membrane pore by amphiphilic peptides. THE JOURNAL OF CHEMICAL PHYSICS 143(24), p. 243115 -
• Schubertova, V; Martinez-Veracoechea, FJ; Vacha, R, 2015: Influence of ligand distribution on uptake efficiency. SOFT MATTER 11(14), p. 2726 - 2730, doi: 10.1039/c4sm02815e
• 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
• 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
• 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
• 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
• 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
• Kozmon, S; Tvaroska, I, 2015: Molecular dynamic studies of amyloid-beta interactions with curcumin and Cu2+ ions. CHEMICAL PAPERS 69(9), p. 1262 - 1276, doi: 10.1515/chempap-2015-0134
• Reblova, K; Kulhanek, P; Fajkusova, L, 2015: Computational study of missense mutations in phenylalanine hydroxylase. JOURNAL OF MOLECULAR MODELING 21(4), doi: 10.1007/s00894-015-2620-6
• 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
• 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

2014

• Varekova, RS; Jaiswal, D; Sehnal, D; Ionescu, CM; Geidl, S; Pravda, L; Horsky, V; Wimmerova, M; Koca, J, 2014: MotiveValidator: interactive web-based validation of ligand and residue structure in biomolecular complexes. NUCLEIC ACIDS RESEARCH 42(W1), p. W227 - W233, doi: 10.1093/nar/gku426
• 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
• Novotny, J; Yurenko, YP; Kulhanek, P; Marek, R, 2014: Tailoring the properties of quadruplex nucleobases for biological and nanomaterial applications. PHYSICAL CHEMISTRY CHEMICAL PHYSICS 16(29), p. 15241 - 15248, doi: 10.1039/c4cp00541d
• Vacha, R; Linse, S; Lund, M, 2014: Surface Effects on Aggregation Kinetics of Amyloidogenic Peptides. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 136(33), p. 11776 - 11782, doi: 10.1021/ja505502e
• Vacha, R; Frenkel, D, 2014: Stability of Bicelles: A Simulation Study. LANGMUIR 30(15), p. 4229 - 4235, doi: 10.1021/la4048159
• Vacha, R; Frenkel, D, 2014: Simulations Suggest Possible Novel Membrane Pore Structure. LANGMUIR 30(5), p. 1304 - 1310, doi: 10.1021/la402727a
• 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
• 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
• 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
• 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
• 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

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
• 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
• Voracova, I; Vanek, J; Pasulka, J; Strelcova, Z; Lubal, P; Hermann, P, 2013: Dissociation kinetics study of copper(II) complexes of DO3A, DOTA and its monosubstituted derivatives. POLYHEDRON 61, p. 99 - 104, doi: 10.1016/j.poly.2013.05.042
• 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
• 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
• 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
• 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
• 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
• Tvaroska, I; Kozmon, S; Wimmerova, M; Koca, J, 2013: A QM/MM Investigation of the Catalytic Mechanism of Metal-Ion-Independent Core 2 beta 1,6-N-Acetylglucosaminyltransferase. CHEMISTRY-A EUROPEAN JOURNAL 19(25), p. 8153 - 8162, doi: 10.1002/chem.201300383
• Berkowitz, M; Irudayam, S; Santo, K; Vacha, R, 2013: Structural and thermodynamic characteristics of melittin-phospholipid bilayer interaction: Results from computer simulations. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 245
• Shi, QX; Bergquist, KE; Huo, RP; Li, JL; Lund, M; Vacha, R; Sundin, A; Butkus, E; Orentas, E; Warnmark, K, 2013: Composition- and Size-Controlled Cyclic Self-Assembly by Solvent- and C-60-Responsive Self-Sorting. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 135(40), p. 15263 - 15268, doi: 10.1021/ja408582w
• Vacha, R; Martinez-Veracoechea, FJ; Frenkel, D, 2013: Challenges in Nanoparticle Delivery: Cellular Uptake and Intracellular Escape. BIOPHYSICAL JOURNAL 104(2), p. 622A - 622A
• Stenqvist, B; Thuresson, A; Kurut, A; Vacha, R; Lund, M, 2013: Faunus - a flexible framework for Monte Carlo simulation. MOLECULAR SIMULATION 39(14-15), p. 1205 - 1211, doi: 10.1080/08927022.2013.828207
• Standara, S; Kulhanek, P; Marek, R; Straka, M, 2013: Xe-129 NMR chemical shift in Xe@C-60 calculated at experimental conditions: Essential role of the relativity, dynamics, and explicit solvent. JOURNAL OF COMPUTATIONAL CHEMISTRY 34(22), p. 1890 - 1898, doi: 10.1002/jcc.23334

2012

• 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
• Cernochova, J; Branna, P; Rouchal, M; Kulhanek, P; Kuritka, I; Vicha, R, 2012: Determination of Intrinsic Binding Modes by Mass Spectrometry: Gas-Phase Behavior of Adamantylated Bisimidazolium Guests Complexed to Cucurbiturils. CHEMISTRY-A EUROPEAN JOURNAL 18(43), p. 13633 - 13637, doi: 10.1002/chem.201201444
• 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
• Vazdar, M; Pluharova, E; Mason, PE; Vacha, R; Jungwirth, P, 2012: Ions at Hydrophobic Aqueous Interfaces: Molecular Dynamics with Effective Polarization. JOURNAL OF PHYSICAL CHEMISTRY LETTERS 3(15), p. 2087 - 2091, doi: 10.1021/jz300805b
• Guerineau, M; Kriz, Z; Kozakova, L; Bednarova, K; Janos, P; Palecek, J, 2012: Analysis of the Nse3/MAGE-Binding Domain of the Nse4/EID Family Proteins. PLOS ONE 7(4), doi: 10.1371/journal.pone.0035813
• Vacha, R; Martinez-Veracoechea, FJ; Frenkel, D, 2012: Intracellular Release of Endocytosed Nanoparticles Upon a Change of Ligand-Receptor Interaction. ACS NANO 6(12), p. 10598 - 10605, doi: 10.1021/nn303508c
• Vacha, R; Marsalek, O; Willard, AP; Bonthuis, DJ; Netz, RR; Jungwirth, P, 2012: Charge Transfer between Water Molecules As the Possible Origin of the Observed Charging at the Surface of Pure Water. JOURNAL OF PHYSICAL CHEMISTRY LETTERS 3(1), p. 107 - 111, doi: 10.1021/jz2014852
• Bieler, NS; Knowles, TPJ; Frenkel, D; Vacha, R, 2012: Connecting Macroscopic Observables and Microscopic Assembly Events in Amyloid Formation Using Coarse Grained Simulations. PLOS COMPUTATIONAL BIOLOGY 8(10), p. ´nestrankovano´ - , doi: 10.1371/journal.pcbi.1002692
• Berkowitz, ML; Vacha, R, 2012: Aqueous Solutions at the Interface with Phospholipid Bilayers. ACCOUNTS OF CHEMICAL RESEARCH 45(1), p. 74 - 82, doi: 10.1021/ar200079x
• 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
• 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
• Vacha, R; Roke, S, 2012: Sodium Dodecyl Sulfate at Water-Hydrophobic Interfaces: A Simulation Study. JOURNAL OF PHYSICAL CHEMISTRY B 116(39), p. 11936 - 11942, doi: 10.1021/jp304900z
• Kammath, VB; Sebej, P; Slanina, T; Kriz, Z; Klan, P, 2012: Photoremovable chiral auxiliary. PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES 11(3), p. 500 - 507, doi: 10.1039/c1pp05096f
• 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
• Pospisil, M; Kovar, P; Vacha, R; Svoboda, M, 2012: Study of the betulin molecule in a water environment; ab initio and molecular simulation calculations. JOURNAL OF MOLECULAR MODELING 18(1), p. 367 - 376, doi: 10.1007/s00894-011-1055-y
• Vacha, R; Marsalek, O; Willard, AP; Bonthuis, DJ; Netz, RR; Jungwirth, P, 2012: Charge transfer between water molecules leads to weak charging at the surface of pure water. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 244
• 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
• 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
• Matuska, R; Kubat, V, 2012: National School-Leaving Examination in Chemistry - The Chemical Point of View. CHEMICKE LISTY 106(4), p. 307 - 311
• 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
• Novotny, J; Kulhanek, P; Marek, R, 2012: Biocompatible Xanthine-Quadruplex Scaffold for Ion-Transporting DNA Channels. JOURNAL OF PHYSICAL CHEMISTRY LETTERS 3(13), p. 1788 - 1792, doi: 10.1021/jz300559w

2011

• Both, P; Sobczak, L; Breton, C; Hann, S; Nobauer, K; Paschinger, K; Kozmon, S; Mucha, J; Wilson, IBH, 2011: Distantly related plant and nematode core alpha 1,3-fucosyltransferases display similar trends in structure-function relationships. GLYCOBIOLOGY 21(11), p. 1401 - 1415, doi: 10.1093/glycob/cwr056
• Vacha, R; Rick, SW; Jungwirth, P; de Beer, AGF; de Aguiar, HB; Samson, JS; Roke, S, 2011: The Orientation and Charge of Water at the Hydrophobic Oil Droplet-Water Interface. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 133(26), p. 10204 - 10210, doi: 10.1021/ja202081x
• Vacha, R; Frenkel, D, 2011: Relation between Molecular Shape and the Morphology of Self-Assembling Aggregates: A Simulation Study. BIOPHYSICAL JOURNAL 101(6), p. 1432 - 1439, doi: 10.1016/j.bpj.2011.07.046
• Standara, S; Kulhanek, P; Marek, R; Hornicek, J; Bour, P; Straka, M, 2011: Simulations of Xe-129 NMR chemical shift of atomic xenon dissolved in liquid benzene. THEORETICAL CHEMISTRY ACCOUNTS 129(42127), p. 677 - 684, doi: 10.1007/s00214-011-0930-z
• Vacha, R; Martinez-Veracoechea, FJ; Frenkel, D, 2011: Receptor-Mediated Endocytosis of Nanoparticles of Various Shapes. NANO LETTERS 11(12), p. 5391 - 5395, doi: 10.1021/nl2030213
• 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
• Vacha, R; Jungwirth, P; Roke, S; Frenkel, D, 2011: Sodium dodecyl sulfate at water/hydrophobic interfaces. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 242
• 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

2010

• Kolman, V; Kulhanek, P; Sindelar, V, 2010: Inclusion of Carboxyl Function Inside of Cucurbiturils and its Use in Molecular Switches. CHEMISTRY-AN ASIAN JOURNAL 5(11), p. 2386 - 2392, doi: 10.1002/asia.201000388
• Olsak, M; Filipovic, J; Prokop, M, 2010: FASTGRID - THE ACCELERATED AUTOGRID POTENTIAL MAPS GENERATION FOR MOLECULAR DOCKING. COMPUTING AND INFORMATICS 29(6), p. 1325 - 1336
• Wolff, W; McKenna, J; Vacha, R; Zohrabi, M; Gaire, B; Carnes, KD; Ben-Itzhak, I, 2010: Three-dimensional energy profile measurement of a molecular ion beam by coincidence momentum imaging compared to a retarding field analyzer. JOURNAL OF INSTRUMENTATION 5, doi: 10.1088/1748-0221/5/10/P10006
• Vacha, R; Jurkiewicz, P; Petrov, M; Berkowitz, ML; Bockmann, RA; Barucha-Kraszewska, J; Hof, M; Jungwirth, P, 2010: Mechanism of Interaction of Monovalent Ions with Phosphatidylcholine Lipid Membranes. JOURNAL OF PHYSICAL CHEMISTRY B 114(29), p. 9504 - 9509, doi: 10.1021/jp102389k
• Lund, M; Jagoda-Cwiklik, B; Woodward, CE; Vacha, R; Jungwirth, P, 2010: Dielectric Interpretation of Specificity of Ion Pairing in Water. JOURNAL OF PHYSICAL CHEMISTRY LETTERS 1(1), p. 300 - 303, doi: 10.1021/jz900151f
• 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
• Vacha, Robert; Horinek, Dominik; Buchner, Richard; Winter, Bernd; Jungwirth, Pavel, 2010: Comment on ´An explanation for the charge on water´s surface´ by A. Gray-Weale and J. K. Beattie, Phys. Chem. Chem. Phys., 2009, 11, 10994. PHYSICAL CHEMISTRY CHEMICAL PHYSICS 12(42), p. 14362 - 14363

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
• Winter, Bernd; Faubel, Manfred; Vacha, Robert; Jungwirth, Pavel, 2009: Reply to comments on Frontiers Article ´Behavior of hydroxide at the water/vapor interface´. CHEMICAL PHYSICS LETTERS 481(2014-03-01T00:00:00.000), p. 19 - 21
• Vacha, Robert; Berkowitz, Max L.; Jungwirth, Pavel, 2009: Molecular Model of a Cell Plasma Membrane With an Asymmetric Multicomponent Composition: Water Permeation and Ion Effects. BIOPHYSICAL JOURNAL 96(11), p. 4493 - 4501
• Ottosson, Niklas; Vacha, Robert; Aziz, Emad F.; Pokapanich, Wandared; Eberhardt, Wolfgang; Svensson, Svante; Ohrwall, Gunnar; Jungwirth, Pavel; Bjorneholm, Olle; Winter, Bernd, 2009: Large variations in the propensity of aqueous oxychlorine anions for the solution/vapor interface. JOURNAL OF CHEMICAL PHYSICS 131(12)
• Vacha, Robert; Megyes, Tunde; Bako, Imre; Pusztai, Laszlo; Jungwirth, Pavel, 2009: Benchmarking Polarizable Molecular Dynamics Simulations of Aqueous Sodium Hydroxide by Diffraction Measurements. JOURNAL OF PHYSICAL CHEMISTRY A 113(16), p. 4022 - 4027
• Winter, Bernd; Faubel, Manfred; Vacha, Robert; Jungwirth, Pavel, 2009: Behavior of hydroxide at the water/vapor interface. CHEMICAL PHYSICS LETTERS 474(2014-06-04T00:00:00.000), p. 241 - 247
• Heyda, Jan; Vacha, Robert; Vondrasek, Jiri; Jungwirth, Pavel, 2009: Ions at aqueous interfaces: From water surface to hydrated proteins. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 237
• Heyda, Jan; Pokorna, Jana; Vrbka, Lubos; Vacha, Robert; Jagoda-Cwiklik, Barbara; Konvalinka, Jan; Jungwirth, Pavel; Vondrasek, Jiri, 2009: Ion specific effects of sodium and potassium on the catalytic activity of HIV-1 protease. PHYSICAL CHEMISTRY CHEMICAL PHYSICS 11(35), p. 7599 - 7604
• Vlachy, Nina; Jagoda-Cwiklik, Barbara; Vacha, Robert; Touraud, Didier; Jungwirth, Pavel; Kunz, Werner, 2009: Hofmeister series and specific interactions of charged headgroups with aqueous ions. ADVANCES IN COLLOID AND INTERFACE SCIENCE 146(2014-02-01T00:00:00.000), p. 42 - 47
• Vacha, Robert; Siu, Shirley W. I.; Petrov, Michal; Boeckmann, Rainer A.; Barucha-Kraszewska, Justyna; Jurkiewicz, Piotr; Hof, Martin; Berkowitz, Max L.; Jungwirth, Pavel, 2009: Effects of Alkali Cations and Halide Anions on the DOPC Lipid Membrane. JOURNAL OF PHYSICAL CHEMISTRY A 113(26), p. 7235 - 7243