Publication Records

OBOŘILOVÁ, Radka, Jakub HRUŠKA, Rahul DEB, Robert VÁCHA and Jan PŘIBYL. AFM Spectroscopy for the Study of Lipid Bilayer Stability and Morphology. In NanoBio and Med 2024, Barcelona. 2024.

PAJTINKA, Peter and Robert VÁCHA. Amphipathic Helices Can Sense Both Positive and Negative Curvatures of Lipid Membranes. Journal of physical chemistry letters. Washington DC: AMER CHEMICAL SOC1155 16TH ST, NW, WASHINGTON, DC 20036, 2024, vol. 15, No 1, p. 175-179. ISSN 1948-7185. Available from: https://dx.doi.org/10.1021/acs.jpclett.3c02785.

DEB, Rahul, Marcelo D T TORRES, Miroslav BOUDNÝ, Marketa KOBERSKA, Floriana CAPPIELLO, Miroslav POPPER, Katerina DVORAKOVA BENDOVA, Martina DRABINOVÁ, Adelheid HANACKOVA, Katy JEANNOT, Milos PETRIK, Maria Luisa MANGONI, Gabriela BALIKOVA NOVOTNA, Marek MRÁZ, Cesar DE LA FUENTE-NUNEZ and Robert VÁCHA. Computational Design of Pore-Forming Peptides with Potent Antimicrobial and Anticancer Activities. Journal of Medicinal Chemistry. Washington: American Chemical Society, 2024, vol. 67, No 16, p. 14040-14061. ISSN 0022-2623. Available from: https://dx.doi.org/10.1021/acs.jmedchem.4c00912.

BARTOŠ, Ladislav, Anant K. MENON and Robert VÁCHA. Insertases scramble lipids: Molecular simulations of MTCH2. Structure. 2024, vol. 2024, No 32, p. 505-510. Available from: https://dx.doi.org/10.1016/j.str.2024.01.012.

KHODAM HAZRATI, Mehrnoosh and Robert VÁCHA. Membrane Adsorption Enhances Translocation of Antimicrobial Peptide Buforin 2. Journal of Physical Chemistry B. WASHINGTON: American Chemical Society, 2024, vol. 128, No 35, p. 8469-8476. ISSN 1520-6106. Available from: https://dx.doi.org/10.1021/acs.jpcb.4c04338.

BLASCO, Sofia, Lukáš SUKENÍK and Robert VÁCHA. Nanoparticle induced fusion of lipid membranes. Nanoscale. CAMBRIDGE: Royal Society of Chemistry, 2024, vol. 16, No 21, p. 10221-10229. ISSN 2040-3364. Available from: https://dx.doi.org/10.1039/d4nr00591k.

BARTOŠ, Ladislav, Martina DRABINOVÁ and Robert VÁCHA. Optimizing properties of translocation-enhancing transmembrane proteins. Biophysical Journal. 2024, vol. 123, No 10, p. 1240-1252. ISSN 0006-3495. Available from: https://dx.doi.org/10.1016/j.bpj.2024.04.009.

BIRIUKOV, Denys and Robert VÁCHA. Pathways to a Shiny Future: Building the Foundation for Computational Physical Chemistry and Biophysics in 2050. Online. ACS PHYSICAL CHEMISTRY AU. WASHINGTON: AMER CHEMICAL SOC, 2024, vol. 4, No 4, p. 302-313. Available from: https://dx.doi.org/10.1021/acsphyschemau.4c00003.

BARTOŠ, Ladislav and Robert VÁCHA. Peptide translocation across asymmetric phospholipid membranes. Biophysical Journal. Cell Press, 2024, vol. 123, No 6, p. 693-702. ISSN 0006-3495. Available from: https://dx.doi.org/10.1016/j.bpj.2024.02.006.

LINHARTOVÁ, Kateřina, Francesco Luca FALGINELLA, Martin MÁTL, Marek ŠEBESTA, Robert VÁCHA and Richard ŠTEFL. Sequence and structural determinants of RNAPII CTD phase-separation and phosphorylation by CDK7. Nature Communications. Berlin: Nature Research, 2024, vol. 15, No 1, p. 1-17. ISSN 2041-1723. Available from: https://dx.doi.org/10.1038/s41467-024-53305-2.

DEB, Rahul, Ivo KABELKA, Jan PŘIBYL and Robert VÁCHA. De novo design of peptides that form transmembrane barrel pores killing antibiotic resistant bacteria. In BPS Annual Meeting 2023. 2023.

BLASCO, Sofia, Lukáš SUKENÍK and Robert VÁCHA. Designing spheroidal nanoparticles to induce membrane fusion of liposomes. In EMBO Workshop Mechanisms of membrane fusion 2023. 2023.

BIRIUKOV, Denys and Matti JAVANAINEN. Efficient Simulations of Solvent Asymmetry Across Lipid Membranes Using Flat-Bottom Restraints. Journal of Chemical Theory and Computation. Washington DC: American Chemical Society, 2023, vol. 19, No 18, p. 6332-6341. ISSN 1549-9618. Available from: https://dx.doi.org/10.1021/acs.jctc.3c00614.

SUKENÍK, Lukáš, Liya MUKHAMEDOVA, Michaela PROCHÁZKOVÁ, Karel ŠKUBNÍK, Pavel PLEVKA and Robert VÁCHA. Elucidating the Mechanisms of Genome Release in Picornaviruses using Cryo-EM and Coarse-Grained Simulations. In EBSA Congress 2023. 2023.

KHODAM HAZRATI, Mehrnoosh and Robert VÁCHA. Membrane adsorption enhances translocation of antimicrobial peptide buforin 2. In EBSA Congress 2023. 2023.

BIRIUKOV, Denys, Riopedre Fernández MIGUEL and Martinez-Seara HECTOR. Model Sugars Right: Improved Interactions of Glycans in All-Atom Molecular Dynamics Simulations. In GGMM 2023 – Young Modellers Conference. 2023.

BIRIUKOV, Denys, Timothée Emmanuel J. RIVEL and Robert VÁCHA. Multiple factors modulating the formation of toroidal membrane pores. In NIVB MEETING 2023. 2023. ISSN 2336-7202.

JAHN, Helene, Ladislav BARTOŠ, Grace I. DEARDEN, Jeremy S. DITTMAN, Joost C. M HOLTHUIS, Robert VÁCHA and Anant K. MENON. Phospholipids are imported into mitochondria by VDAC, a dimeric beta barrel scramblase. Nature Communications. Heidelberger: Nature Research, 2023, vol. 14, No 1, p. 1-16. ISSN 2041-1723. Available from: https://dx.doi.org/10.1038/s41467-023-43570-y.

LIRUSSI, Frederic, Kyrylo PYRSHEV, Semen YESYLEVSKYY, Timothée Emmanuel Jonathan RIVEL, Tatiana LOPEZ, Eleonore COPPENS, Simona MURA, Patrick COUVREUR and Christophe RAMSEYER. Plasma membrane lipid bilayer is druggable: Selective delivery of gemcitabine-squalene nano-medicine to cancer cells. Biochimica et Biophysica Acta - Molecular Basis of Disease. Amsterdam: ELSEVIER SCIENCE BV, 2023, vol. 1869, No 2, p. 1-12. ISSN 0925-4439. Available from: https://dx.doi.org/10.1016/j.bbadis.2022.166614.

VAZDAR, K., C. TEMPRA, A. OLŻYŃSKA, Denys BIRIUKOV, L. CWIKLIK and M. VAZDAR. Stealthy Player in Lipid Experiments? EDTA Binding to Phosphatidylcholine Membranes Probed by Simulations and Monolayer Experiments. Journal of Physical Chemistry B. WASHINGTON: American Chemical Society, 2023, vol. 127, No 24, p. 5462-5469. ISSN 1520-6106. Available from: https://dx.doi.org/10.1021/acs.jpcb.3c03207.

FALGINELLA, Francesco Luca, Marek KRAVEC, Martina DRABINOVÁ, Petra PACLÍKOVÁ, Vítězslav BRYJA and Robert VÁCHA. Binding of DEP domain to phospholipid membranes: More than just electrostatics. Biochimica et Biophysica Acta (BBA) - Biomembranes. Amsterdam: Elsevier, 2022, vol. 1864, No 10, p. 1-12. ISSN 0005-2736. Available from: https://dx.doi.org/10.1016/j.bbamem.2022.183983.

DEB, Rahul, Ivo KABELKA, Jan PŘIBYL and Robert VÁCHA. De novo design of peptides that form transmembrane barrel pores killing antibiotic resistant bacteria. 2022.

SUKENÍK, Lukáš, Rahul DEB and Robert VÁCHA. HOW LARGE MOLECULES CAN ENTER CELL. In Czech Chemical Society Symposium Series - Annual meeting of the National Institute of Virology and Bacteriology (NIVB). 2022. ISSN 2336-7202.

KABELKA, Ivo, Vasil GEORGIEV, Lisa MARX, Peter PAJTINKA, Karl LOHNER, Georg PABST, Rumiana DIMOVA and Robert VÁCHA. Magainin 2 and PGLa in Bacterial Membrane Mimics III: Membrane Fusion and Disruption. Biophysical Journal. New York, USA: Cell Press, 2022, vol. 121, No 5, p. 852-861. ISSN 0006-3495. Available from: https://dx.doi.org/10.1016/j.bpj.2021.12.035.

SEMERARO, E.F., Peter PAJTINKA, L. MARX, Ivo KABELKA, R. LEBER, K. LOHNER, Robert VÁCHA and G. PABST. Magainin 2 and PGLa in bacterial membrane mimics IV: Membrane curvature and partitioning. BIOPHYSICAL JOURNAL. UNITED STATES: CELL PRESS, 2022, vol. 121, No 23, p. 4689-4701. ISSN 0006-3495. Available from: https://dx.doi.org/10.1016/j.bpj.2022.10.018.

PETERKOVÁ, Kateřina, Ivo DURNÍK, Radek MAREK, Janez PLAVEC and Peter PODBEVŠEK. Pyrene-Lablled G-Quadruplexes Derived from the KIT Proto-Oncogene. In 35th Central European NMR Meeting, VALTICE, 2022. 2022.

PETERKOVÁ, Kateřina, Ivo DURNÍK, Radek MAREK, Janez PLAVEC and Peter PODBEVŠEK. Structural analysis of pyrene-labelled G-quadruplexes derived from the KIT proto-oncogene. In XIIth International conference, NMR: a tool for biology, Institut Pasteur. 2022.

KHIRSARIYA, PrashantKumar, Patrik POSPÍŠIL, Lukáš MAIER, Miroslav BOUDNÝ, Martin BABÁŠ, Ondřej KROUTIL, Marek MRÁZ, Robert VÁCHA and Kamil PARUCH. Synthesis and Profiling of Highly Selective Inhibitors of Methyltransferase DOT1L Based on Carbocyclic C-Nucleosides. Journal of Medicinal Chemistry. Washington: American Chemical Society, 2022, vol. 65, No 7, p. 5701-5723. ISSN 0022-2623. Available from: https://dx.doi.org/10.1021/acs.jmedchem.1c02228.

DRABINOVÁ, Martina, Martina ČARNECKÁ, Otakar HUMPA, Iva SLANINOVÁ and Jiří SLANINA. Acetylace 7-hydroxy skupiny dibenzocyklooktadienových lignanů zvyšuje inhibici P-glykoproteinu (Acetylation of 7-hydroxygroup of dibenzocyclooktadiene lignans increases inhibition of P-glycoprotein). In 65. Studentská vědecká konference - program a sborník abstraktů. 2021. ISBN 978-80-210-6313-6.

KABELKA, Ivo and Robert VÁCHA. Advances in Molecular Understanding of α-helical Membrane-Active Peptides. Accounts of chemical research. American Chemical Society, 2021, vol. 54, No 9, p. 2196-2204. ISSN 0001-4842. Available from: https://dx.doi.org/10.1021/acs.accounts.1c00047.

ŠKUBNÍK, Karel, Lukáš SUKENÍK, David BUCHTA, Tibor FÜZIK, Michaela PROCHÁZKOVÁ, Jana MORAVCOVÁ, Lenka ŠMERDOVÁ, Antonín PŘIDAL, Robert VÁCHA and Pavel PLEVKA. Capsid opening enables genome release of iflaviruses. Science advances. New York: American Association for the Advancement of Science, 2021, vol. 7, No 1, p. 1-9. ISSN 2375-2548. Available from: https://dx.doi.org/10.1126/sciadv.abd7130.

PROCHÁZKOVÁ, Michaela, Tibor FÜZIK, Danyil GRYBCHUK, Francesco Luca FALGINELLA, Lucie PODEŠVOVÁ, Vyacheslav YURCHENKO, Robert VÁCHA and Pavel PLEVKA. Capsid Structure of Leishmania RNA Virus 1. Journal of Virology. American Society for Microbiology, 2021, vol. 95, No 3, p. "e01957", 12 pp. ISSN 0022-538X. Available from: https://dx.doi.org/10.1128/JVI.01957-20.

LABAJOVA, N., N. BARANOVA, Miroslav JURÁSEK, Robert VÁCHA, M. LOOSE and I. BARAK. Cardiolipin-Containing Lipid Membranes Attract the Bacterial Cell Division Protein DivIVA. International Journal of Molecular Sciences. Basel: Multidisciplinary Digital Publishing Institute, 2021, vol. 22, No 15, p. 8350-8370. ISSN 1422-0067. Available from: https://dx.doi.org/10.3390/ijms22158350.

SUKENÍK, Lukáš, Liya MUKHAMEDOVA, Michaela PROCHÁZKOVÁ, Karel ŠKUBNÍK, Pavel PLEVKA and Robert VÁCHA. Cargo Release from Nonenveloped Viruses and Virus-like Nanoparticles: Capsid Rupture or Pore Formation. ACS Nano. Washington, D.C.: American Chemical Society, 2021, vol. 15, No 12, p. 19233-19243. ISSN 1936-0851. Available from: https://dx.doi.org/10.1021/acsnano.1c04814.

BARTOŠ, Ladislav, Ivo KABELKA and Robert VÁCHA. Enhanced translocation of amphiphilic peptides across membranes by transmembrane proteins. Biophysical Journal. New York, USA: Cell Press, 2021, vol. 120, No 11, p. 2296-2305. ISSN 0006-3495. Available from: https://dx.doi.org/10.1016/j.bpj.2021.04.005.

PEŠKA, Vratislav, Petr FAJKUS, Michal BUBENÍK, Václav BRÁZDA, Natália BOHÁLOVÁ, Vojtěch DVOŘÁČEK, Jiří FAJKUS and Sonia GARCIA. Extraordinary diversity of telomeres, telomerase RNAs and their template regions in Saccharomycetaceae. Scientific Reports. Nature Research, 2021, vol. 11, No 1, p. "12784", 11 pp. ISSN 2045-2322. Available from: https://dx.doi.org/10.1038/s41598-021-92126-x.

SAVENKO, M., Timothée Emmanuel J. RIVEL, S. YESYLEVSKYY and C. RAMSEYER. Influence of Substrate Hydrophilicity on Structural Properties of Supported Lipid Systems on Graphene, Graphene Oxides, and Silica. Journal of Physical Chemistry B. Washington, D.C.: American Chemical Society, 2021, vol. 125, No 29, p. 8060-8074. ISSN 1520-6106. Available from: https://dx.doi.org/10.1021/acs.jpcb.1c04615.

JURÁSEK, Miroslav, Jitender KUMAR, Petra PACLÍKOVÁ, Alka Kumari JADAUN, Konstantinos TRIPSIANES, Vítězslav BRYJA and Robert VÁCHA. Phosphorylation-induced changes in the PDZ domain of Dishevelled 3. Scientific Reports. NATURE PUBLISHING GROUP, 2021, vol. 11, No 1, p. "1484", 14 pp. ISSN 2045-2322. Available from: https://dx.doi.org/10.1038/s41598-020-79398-5.

KABELKA, Ivo, Radim BROŽEK and Robert VÁCHA. Selecting Collective Variables and Free Energy Methods for Peptide Translocation Across Membranes. Journal of Chemical Information and Modeling. USA, 2021, vol. 61, No 2, p. 819-830. ISSN 1549-9596. Available from: https://dx.doi.org/10.1021/acs.jcim.0c01312.

SARMENTO, M.J., Michael Christopher OWEN, J.C. RICARDO, B. CHMELOVÁ, D. DAVIDOVIĆ, I. MIKHALYOV, N. GRETSKAYA, M. HOF, M. AMARO, Robert VÁCHA and R. ŠACHL. The impact of the glycan headgroup on the nanoscopic segregation of gangliosides. Biophysical Journal. New York, USA: Cell Press, 2021, vol. 120, No 24, p. 5530-5543. ISSN 0006-3495. Available from: https://dx.doi.org/10.1016/j.bpj.2021.11.017.

TÜRKOVÁ, Alžběta, Ivo KABELKA, Tereza KRÁLOVÁ, Lukáš SUKENÍK, Šárka POKORNÁ, Martin HOF and Robert VÁCHA. Effect of helical kink in antimicrobial peptides on membrane pore formation. eLife. Cambridge: eLife Sciences Publications Ltd, 2020, vol. 9, March 2020, p. 1-38. ISSN 2050-084X. Available from: https://dx.doi.org/10.7554/eLife.47946.

BROŽEK, Radim, Ivo KABELKA and Robert VÁCHA. Effect of Helical Kink on Peptide Translocation across Phospholipid Membranes. The Journal of Physical Chemistry B. Washington, D.C.: American Chemical Society, 2020, vol. 124, No 28, p. 5940-5947. ISSN 1520-6106. Available from: https://dx.doi.org/10.1021/acs.jpcb.0c03291.

JURÁSEK, Miroslav, Klas FLÄRDH and Robert VÁCHA. Effect of membrane composition on DivIVA-membrane interaction. BBA Biomembranes. Amsterdam: Elsevier, 2020, vol. 1862, No 8, p. 1-9. ISSN 0005-2736. Available from: https://dx.doi.org/10.1016/j.bbamem.2019.183144.

ZAPLETAL, Vojtěch, Arnošt MLÁDEK, Kateřina BENDOVÁ, Petr LOUŠA, Erik NOMILNER, Zuzana JASEŇÁKOVÁ, Vojtěch KUBÁŇ, Markéta MAKOVICKÁ, Alice LANÍKOVÁ, Lukáš ŽÍDEK and Jozef HRITZ. Choice of Force Field for Proteins Containing Structured and Intrinsically Disordered Regions. Biophysical Journal. Bethesda, USA: Biophysical Society, 2020, vol. 118, No 7, p. 1621-1633. ISSN 0006-3495. Available from: https://dx.doi.org/10.1016/j.bpj.2020.02.019.

KABELKA, Ivo, Michael PACHLER, Sylvain PRÉVOST, Ilse LETOFSKY-PAPST, Karl LOHNER, Georg PABST and Robert VÁCHA. Magainin 2 and PGLa in Bacterial Membrane Mimics II: Membrane Fusion and Sponge Phase Formation. Biophysical Journal. Cambridge, USA: Cell Press, 2020, vol. 118, No 3, p. 612-623. ISSN 0006-3495. Available from: https://dx.doi.org/10.1016/j.bpj.2019.12.019.

FATAFTA, H., C. POOJARI, A. SAYYED-AHMAD, B. STRODEL and Michael Christopher OWEN. Role of Oxidized Gly25, Gly29, and Gly33 Residues on the Interactions of A beta(1-42) with Lipid Membranes. ACS CHEMICAL NEUROSCIENCE. WASHINGTON: AMER CHEMICAL SOC, 2020, vol. 11, No 4, p. 535-548, 27 pp. ISSN 1948-7193. Available from: https://dx.doi.org/10.1021/acschemneuro.9b00558.

TÜRKOVÁ, Alžběta, Ivo KABELKA, Lukáš SUKENÍK, Šárka POKORNÁ, Martin Peter HOF and Robert VÁCHA. ROLE OF PROLINE/GLYCINE KINK IN PORE FORMATION BY ANTIMICROBIAL PEPTIDES. In XXth INTERDISCIPLINARY MEETING OF YOUNG RESEARCHERS AND STUDENTS IN THE FIELD OF CHEMISTRY, BIOCHEMISTRY, MOLECULAR BIOLOGY, AND BIOMATERIALS. 2020. ISSN 2336-7202.

BRÁZDA, Pavel, Magdaléna KREJČÍKOVÁ, Aiste KASILIAUSKAITE, Eliška ŠMIŘÁKOVÁ, Tomáš KLUMPLER, Robert VÁCHA, Karel KUBÍČEK and Richard ŠTEFL. Yeast Spt6 Reads Multiple Phosphorylation Patterns of RNA Polymerase II C-Terminal Domain In Vitro. Journal of Molecular Biology. Academic Press, 2020, vol. 432, No 14, p. 4092-4107. ISSN 0022-2836. Available from: https://dx.doi.org/10.1016/j.jmb.2020.05.007.

HARNOŠ, Jakub, M.C.A. CANIZAL, Miroslav JURÁSEK, Jitender KUMAR, Cornelia HOLLER, Alexandra SCHAMBONY, Kateřina HANÁKOVÁ, Ondřej BERNATÍK, Zbyněk ZDRÁHAL, Kristína GÖMÖRYOVÁ, Tomáš GYBEĽ, Tomasz Witold RADASZKIEWICZ, Marek KRAVEC, Lukáš TRANTÍREK, Jan RYNEŠ, Zankruti DAVE, Ana Iris FERNANDEZ-LLAMAZARES, Robert VÁCHA, Konstantinos TRIPSIANES, Carsten HOFFMANN and Vítězslav BRYJA. Dishevelled-3 conformation dynamics analyzed by FRET-based biosensors reveals a key role of casein kinase 1. Nature Communications. London: Nature Publishing Group, 2019, vol. 10, APR 18 2019, p. 1-18. ISSN 2041-1723. Available from: https://dx.doi.org/10.1038/s41467-019-09651-7.

OWEN, Michael Christopher, D. GNUTT, M.M. GAO, S.K.T.S. WARMLANDER, J. JARVET, A. GRASLUND, R. WINTER, S. EBBINGHAUS and B. STRODEL. Effects of in vivo conditions on amyloid aggregation. Chemical Society Reviews. Cambridge: RSC Publishing, 2019, vol. 48, No 14, p. 3946-3996. ISSN 0306-0012. Available from: https://dx.doi.org/10.1039/c8cs00034d.

BUCHTA, David, Tibor FÜZIK, Dominik HREBÍK, Yevgen LEVDANSKY, Lukáš SUKENÍK, Liya MUKHAMEDOVA, Jana MORAVCOVÁ, Robert VÁCHA and Pavel PLEVKA. Enterovirus particles expel capsid pentamers to enable genome release. Nature Communications. London: Nature Publishing Group, 2019, vol. 10, MAR, p. 1-9. ISSN 2041-1723. Available from: https://dx.doi.org/10.1038/s41467-019-09132-x.

OWEN, Michael Christopher, Andreas KARNER, Radek ŠACHL, Johannes PREINER, Mariana AMARO and Robert VÁCHA. Force Field Comparison of GM1 in a DOPC Bilayer Validated with AFM and FRET Experiments. JOURNAL OF PHYSICAL CHEMISTRY B. Washington, D.C.: American Chemical Society, 2019, vol. 123, No 35, p. 7504-7517. ISSN 1520-6106. Available from: https://dx.doi.org/10.1021/acs.jpcb.9b05095.

TÜRKOVÁ, Alžběta, Ivo KABELKA, Tereza KRÁLOVÁ, Lukáš SUKENÍK, S. POKORNÁ, M. HOF and Robert VÁCHA. Kink in Helical Peptides Affects Membrane Pore Formation. 2019. ISSN 0006-3495. Available from: https://dx.doi.org/10.1016/j.bpj.2018.11.2760.

PACHLER, Michael, Ivo KABELKA, Marie-Sousai APPAVOU, Karl LOHNER, Robert VÁCHA and Georg PABST. Magainin 2 and PGLa in Bacterial Membrane Mimics I: Peptide-Peptide and Lipid-Peptide Interactions. Biophysical Journal. New York: Cell Press, 2019, vol. 117, No 10, p. 1858-1869. ISSN 0006-3495. Available from: https://dx.doi.org/10.1016/j.bpj.2019.10.022.

HAMID, A.K.M., J.C. SALVATORE, K. WANG, P. MURAHARI, A. GULJAS, A. RAGYANSZKI, Michael Christopher OWEN, B. JOJART, M. SZORI, I.G. CSIZMADIA, B. VISKOLCZ and B. FISER. Oxidatively-mediated in silico epimerization of a highly amyloidogenic segment in the human calcitonin hormone (hCT(15-19)). COMPUTATIONAL BIOLOGY AND CHEMISTRY. OXFORD: ELSEVIER SCI LTD, 2019, vol. 80, JUN, p. 259-269. ISSN 1476-9271. Available from: https://dx.doi.org/10.1016/j.compbiolchem.2019.04.005.

PAVLÍKOVÁ PŘECECHTĚLOVÁ, Jana, Arnošt MLÁDEK, Vojtěch ZAPLETAL and Jozef HRITZ. Quantum Chemical Calculations of NMR Chemical Shifts in Phosphorylated Intrinsically Disordered Proteins. Journal of Chemical Theory and Computation. Washington DC: American Chemical Society, 2019, vol. 15, No 10, p. 5642-5658. ISSN 1549-9618. Available from: https://dx.doi.org/10.1021/acs.jctc.8b00257.

PACHLER, M., Ivo KABELKA, R. LEBER, I. LETOFSKY-PAPST, K. LOHNER, Robert VÁCHA and G. PABST. Synergism of Magainins is Not Coupled to the Formation of a Well-Defined Peptide Pore. In 63rd Annual Meeting of the Biophysical-Society. 2019. ISSN 0006-3495. Available from: https://dx.doi.org/10.1016/j.bpj.2018.11.280.

VÁCHA, Robert. Toxicita a aktivita antimikrobiálních peptidů (Toxicity and activity of antimicrobial peptides). Masarykova univerzita, 2019.

LIAO, Q.H., Michael Christopher OWEN, S. BALI, B. BARZ and B. STRODEL. A beta under stress: the effects of acidosis, Cu2+-binding, and oxidation on amyloid beta-peptide dimers. Chemical communications. Cambridge: Royal Society of Chemistry, 2018, vol. 54, No 56, p. 7766-7769. ISSN 1359-7345. Available from: https://dx.doi.org/10.1039/c8cc02263a.

TESEI, Giulio, Erik HELLSTRAND, Kalyani SANAGAVARAPU, Sara LINSE, Emma SPARR, Robert VÁCHA and Mikael LUND. Aggregate Size Dependence of Amyloid Adsorption onto Charged Interfaces. Langmuir. WASHINGTON: AMER CHEMICAL SOC, 1155 16TH ST, NW, WASHINGTON, DC 20036 USA, 2018, vol. 34, No 4, p. 1266-1273. ISSN 0743-7463. Available from: https://dx.doi.org/10.1021/acs.langmuir.7b03155.

ŠTĚPÁN, Jakub, Ivo KABELKA, Jaroslav KOČA and Petr KULHÁNEK. Behavior of BsoBI endonuclease in the presence and absence of DNA. Journal of Molecular Modeling. New York: Springer, 2018, vol. 24, No 1, p. 22-31. ISSN 1610-2940. Available from: https://dx.doi.org/10.1007/s00894-017-3557-8.

HRITZ, Jozef and Arnošt MLÁDEK. Computational Molecular Modeling Techniques of Biomacromolecular Systems. Online. In Jan Hejátko, Toshio Hakoshima. Plant Structural Biology: Hormonal Regulations. 1st ed. CHAM: SPRINGER INT PUBLISHING AG, 2018, p. 295-322. n/a. ISBN 978-3-319-91352-0. Available from: https://dx.doi.org/10.1007/978-3-319-91352-0_15.

OWEN, Michael Christopher, W. KULIG, T. ROG, I. VATTULAINEN and B. STRODEL. Cholesterol Protects the Oxidized Lipid Bilayer from Water Injury: An All-Atom Molecular Dynamics Study. JOURNAL OF MEMBRANE BIOLOGY. NEW YORK: SPRINGER, 2018, vol. 251, No 3, p. 521-534. ISSN 0022-2631. Available from: https://dx.doi.org/10.1007/s00232-018-0028-9.

TUBIANA, L., Miroslav JURÁSEK and I. COLUZZA. Implementing efficient concerted rotations using Mathematica and C code. EUROPEAN PHYSICAL JOURNAL E. NEW YORK: SPRINGER, 2018, vol. 41, No 7, p. 87-95. ISSN 1292-8941. Available from: https://dx.doi.org/10.1140/epje/i2018-11694-7.

KABELKA, Ivo and Robert VÁCHA. Optimal Hydrophobicity and Reorientation of Amphiphilic Peptides Translocating through Membrane. Biophysical Journal. New York, USA: Cell Press, 2018, vol. 115, No 6, p. 1045-1054. ISSN 0006-3495. Available from: https://dx.doi.org/10.1016/j.bpj.2018.08.012.

BOŘILOVÁ LINHARTOVÁ, Petra, Ladislava BARTOŠOVÁ, Adam KŘENEK, Ladislav BARTOŠ, Jiří DOLINA, Filip MAREK, Zdeněk KALA and Lydie IZAKOVIČOVÁ HOLLÁ. Personalizovaná terapie pacientů s gastroezofageální refluxní chorobou - metodika stanovení genového profilu CYP2C19 (Personalized therapy in patients with gastroesophageal reflux disease - methodology of CYP2C19 gene profile´s determination). Gastroenterologie a Hepatologie. Praha: Ambit Media, 2018, vol. 72, No 4, p. 320-328. ISSN 1804-7874. Available from: https://dx.doi.org/10.14735/amgh2018320.

OWEN, Michael Christopher, W. KULIG, C. POOJARI, T. ROG and B. STRODEL. Physiologically-relevant levels of sphingomyelin, but not GM1, induces a beta-sheet-rich structure in the amyloid-beta(1-42) monomer. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES. AMSTERDAM: ELSEVIER SCIENCE BV, 2018, vol. 1860, No 9, p. 1709-1720. ISSN 0005-2736. Available from: https://dx.doi.org/10.1016/j.bbamem.2018.03.026.

LEBER, R., M. PACHLER, Ivo KABELKA, I. SVOBODA, D. KOLLER, Robert VÁCHA, K. LOHNER and G. PABST. Synergism of Antimicrobial Frog Peptides Couples to Membrane Intrinsic Curvature Strain. Biophysical Journal. New York, USA: Cell Press, 2018, vol. 114, No 8, p. 1945-1954. ISSN 0006-3495. Available from: https://dx.doi.org/10.1016/j.bpj.2018.03.006.

ZAPLETAL, Vojtěch, Arnošt MLÁDEK, Jozef HRITZ and Lukáš ŽÍDEK. Computational characterization of hybrid proteins containing ordered and intrinsically disordered regions. In 42nd Congress of the Federation-of-European-Biochemical-Societies (FEBS) on From Molecules to Cells and Back. 2017. ISSN 1742-464X.

SCHUBERTOVÁ, Veronika, F.J. MARTINEZ-VERACOECHEA and Robert VÁCHA. Design of Multivalent Inhibitors for Preventing Cellular Uptake. Scientific Reports. London: Nature Publishing Group, 2017, vol. 7, SEP, p. 11689-11695. ISSN 2045-2322. Available from: https://dx.doi.org/10.1038/s41598-017-11735-7.

MANZANO, Susana, Zoraida MEGÍAS, Cecilia MARTÍNEZ, Alicia GARCÍA, Encarnación AGUADO, Tarik CHILEH, Diego LÓPEZ-ALONSO, Federico GARCÍA-MAROTO, Eduard KEJNOVSKÝ, Jiří ŠIROKÝ, Zdeněk KUBÁT and Tereza KRÁLOVÁ. Overexpression of a flower-specific aerolysin-like protein from the dioecious plant Rumex acetosa alters flower development and induces male sterility in transgenic tobacco. The Plant Journal. 2017, vol. 89, p. 58-72. Available from: https://dx.doi.org/10.1111/tpj.13322.

JURÁSEK, Miroslav and Robert VÁCHA. Self-assembled clusters of patchy rod-like molecules. SOFT MATTER. CAMBRIDGE: ROYAL SOC CHEMISTRY, 2017, vol. 13, No 41, p. 7492-7497. ISSN 1744-683X. Available from: https://dx.doi.org/10.1039/c7sm01384a.

VÁCHA, Robert. Anomalous Fibril Interaction with Surfaces. In CECAM workshop "Multiscale modeling of biomolecular aggregation and protein-membrane interactions in amyloid diseases". 2016.

VÁCHA, Robert. Anomalous Fibril Interaction with Surfaces. 2016.

VÁCHA, Robert. Efficiency of Nanoparticle Uptake Influenced by Multivalent Inhibitors or Ligand Distribution. In Biomembrane days 2016. 2016.

AMARO, Mariana, Radek ŠACHL, Gokcan AYDOGAN, Ilya I. MIKHALYOV, Robert VÁCHA and Martin HOF. (GM1) Ganglioside Inhibits beta-Amyloid Oligomerization Induced bySphingomyelin. Angewandte Chemie International Edition. WEINHEIM: Wiley-V C H VERLAG GMBH, 2016, vol. 55, No 32, p. 9411-9415. ISSN 1433-7851. Available from: https://dx.doi.org/10.1002/anie.201603178.

VÁCHA, Robert. Influence of ligand distribution on the efficiency of nanoparticle uptake. In 10th European Biophysics Congress. 2016.

VÁCHA, Robert. Peptide Features Determining its Ability of Translocation and Membrane Pore Formation. In 6th International Meeting on Antimicrobial Peptides (IMAP2016). 2016.

VÁCHA, Robert. Peptide Features Determining its Translocation and Pore Formation. In Liposomes, Exosomes, and Virosomes: From Modeling Complex Membrane Processes to Medical Diagnostics and Drug Delivery. 2016.

AMARO, M., R. SACHL, G. AYDOGAN, I. MIKHALYOV, Robert VÁCHA and Martin Peter HOF. The role of ganglioside GM1 and sphingomyelin in the oligomerisation of beta-amyloid at physiological conditions: a single molecule study. 2016. ISSN 1742-464X.

VÁCHA, Robert. Influence of ligand distribution on nanoparticle uptake effciency. In 3rd European Joint Theory/Experiment Meeting on Membranes – EJTEMM15. 2015.

SCHUBERTOVÁ, Veronika, Francisco J. MARTINEZ-VERACOECHEA and Robert VÁCHA. Influence of ligand distribution on uptake efficiency. SOFT MATTER. CAMBRIDGE: ROYAL SOC CHEMISTRY, 2015, vol. 11, No 14, p. 2726-2730. ISSN 1744-683X. Available from: https://dx.doi.org/10.1039/c4sm02815e.

KABELKA, Ivo and Robert VÁCHA. Optimal conditions for opening of membrane pore by amphiphilic peptides. JOURNAL OF CHEMICAL PHYSICS. Melville (USA): AMER INST PHYSICS, 2015, vol. 143, No 24, p. nestránkováno, 6 pp. ISSN 0021-9606. Available from: https://dx.doi.org/10.1063/1.4933229.

KRUSE, Holger, Arnošt MLÁDEK, Konstantinos GKIONIS, Andreas HANSEN, Sstefan GRIMME and Jiří ŠPONER. Quantum Chemical Benchmark Study on 46 RNA Backbone Families Using a Dinucleotide Unit. Journal of Chemical Theory and Computation. Washington DC: American Chemical Society, 2015, vol. 11, No 10, p. 4972-4991. ISSN 1549-9618. Available from: https://dx.doi.org/10.1021/acs.jctc.5b00515.

VÁCHA, Robert. Self-assembly of prolate patchy particles. In CECAM workshop on The Physics of Protein Self-Assembly. 2015.

VÁCHA, Robert. Self-assembly of prolate patchy particles. In Gordon Research Conference on „Self-Assembly & Supramolecular Chemistry. 2015.

VÁCHA, Robert. Double-belt a Novel Structure of Membrane Pore. In 2nd European Joint Theoretical/Experimental Meeting on Membranes. 2014.

VÁCHA, Robert and D FRENKEL. Double-belt a Novel Structure of Membrane Pore. In 4th International Meeting on Antimicrobial Peptides (IMAP). 2014.

VÁCHA, Robert and D FRENKEL. Double-belt a Novel Structure of Membrane Pore. In The Physics of Soft and Biological Matter. 2014.

VÁCHA, Robert and D FRENKEL. Double-belt a Novel Structure of Membrane Pore. In CECAM workshop - How proteins can shape and sense membranes--a closer look at hybrid models. 2014.

VÁCHA, Robert and D FRENKEL. Double-belt a Novel Structure of Membrane Pore. In 58th Annual Meeting of the Biophysical Society. 2014.

VÁCHA, Robert, Frank UHLIG and Pavel JUNGWIRTH. Charges at Aqueous Interfaces: Development of Computational Approaches in Direct Contact with Experiment. In S. A. Rice and A. R. Dinner. Advances in Chemical Physics. Hoboken: John Wiley & Sons, Inc., 2014, p. 69-95. Volume 155. ISBN 978-1-118-75577-8. Available from: https://dx.doi.org/10.1002/9781118755815.ch02.

VÁCHA, Robert, S LINSE and M LUND. Physics of colloidal particles with heterogeneously patterned surfaces. In CECAM workshop - Physics of colloidal particles with heterogeneously patterned surfaces. 2014.

VÁCHA, Robert and D. FRENKEL. Simulations Suggest Possible Novel Membrane Pore Structure. Langmuir. Washington D.C.: Amer Chemical Soc, 2014, vol. 30, No 5, p. 1304-1310. ISSN 0743-7463. Available from: https://dx.doi.org/10.1021/la402727a.

VÁCHA, Robert and D. FRENKEL. Stability of Bicelles: A Simulation Study. Langmuir. WASHINGTON: AMER CHEMICAL SOC, 1155 16TH ST, NW, WASHINGTON, DC 20036 USA, 2014, vol. 30, No 15, p. 4229-4235. ISSN 0743-7463. Available from: https://dx.doi.org/10.1021/la4048159.

VÁCHA, Robert, S. LINSE and M. LUND. Surface Effects on Aggregation Kinetics of Amyloidogenic Peptides. Journal of the American Chemical Society. Washington, D.C.: American Chemical Society, 2014, vol. 136, No 33, p. 11776-11782. ISSN 0002-7863. Available from: https://dx.doi.org/10.1021/ja505502e.

VÁCHA, Robert, S LINSE and M LUND. Surface Effects on Aggregation Kinetics of Amyloidogenic Peptides. In CECAM workshop - Molecular and coarse-grained modelling of interactions at bio-nano interface. 2014.

VÁCHA, Robert, S LINSE and M LUND. Surface Effects on Aggregation Kinetics of Amyloidogenic Peptides. In CECAM workshop - Protein assemblies at the interface of functionalised materials. 2014.

SHI, Q., K.-E. BERGQUIST, R. HUO, J. LI, M. LUND, Robert VÁCHA, A. SUNDIN, E. BUTKUS, E. ORENTAS and K. WÄRNMARK. Composition- and Size-Controlled Cyclic Self-Assembly by Solvent- and C60-Responsive Self-Sorting. J AM CHEM SOC. Washington: American Chemical Society, 2013, vol. 135, No 40, p. 15263-15268. ISSN 0002-7863. Available from: https://dx.doi.org/10.1021/ja408582w.

STENQVIST, Bjoern, Axel THURESSON, Anil KURUT, Robert VÁCHA and Mikael LUND. Faunus - a flexible framework for Monte Carlo simulation. Molecular Simulation. Oxon: Taylor & Francis, 2013, vol. 39, 14-15, p. 1205-1211. ISSN 0892-7022. Available from: https://dx.doi.org/10.1080/08927022.2013.828207.

VÁCHA, Robert, F. J. MARTINEZ-VERACOECHEA and D. FRENKEL. Challenges in Nanoparticle Delivery: Cellular Uptake and Intracellular Escape. In Biophysical Society 57th Annual Meeting. 2013.

VÁCHA, Robert. Self-assembly of amphiphilic peptides and their interaction with membranes. In TAPPO workshop. 2013.

VÁCHA, Robert, F. J. MARTINEZ-VERACOECHEA and D. FRENKEL. Simulations of cellular uptake of nanoparticles with various shapes. In International Soft Matter Conference. 2013.

BERKOWITZ, M. L. and Robert VÁCHA. Aqueous Solutions at the Interface with Phospholipid Bilayers. Accounts of chemical research. Washington: American Chemical Society, 2012, vol. 45, No 1, p. 74-82. ISSN 0001-4842. Available from: https://dx.doi.org/10.1021/ar200079x.

BIELER, Noah S., Tuomas P.J. KNOWLES, Daan FRENKEL and Robert VÁCHA. Connecting Macroscopic Observables and Microscopic Assembly Events in Amyloid Formation Using Coarse Grained Simulations. PLOS Computational Biology. San Francisco: PLOS, 2012, vol. 8, No 10, p. "nestránkováno", 10 pp. ISSN 1553-7358. Available from: https://dx.doi.org/10.1371/journal.pcbi.1002692.

VÁCHA, Robert, Ondrej MARSALEK, A.P. WILLARD, D.J. BONTHUIS, R.R. NETZ and Pavel JUNGWIRTH. Charge Transfer between Water Molecules As the Possible Origin of the Observed Charging at the Surface of Pure Water. Journal of Physical Chemistry Letters. Washington: American Chemical Society, 2012, vol. 3, No 1, p. 107–111. ISSN 1948-7185. Available from: https://dx.doi.org/10.1021/jz20148521.

VÁCHA, Robert, Francisco J. MARTINEZ-VERACOECHEA and Daan FRENKEL. Intracellular Release of Endocytosed Nanoparticles Upon a Change of Ligand-Receptor Interaction. ACS Nano. WASHINGTON: American Chemical Society, 2012, vol. 6, No 12, p. 10598-10605. ISSN 1936-0851. Available from: https://dx.doi.org/10.1021/nn303508c.

VAZDAR, Mario, Eva PLUHAŘOVÁ, Phil E MASON, Robert VÁCHA and Pavel JUNGWIRTH. Ions at Hydrophobic Aqueous Interfaces: Molecular Dynamics with Effective Polarization. Journal of Physical Chemistry Letters. WASHINGTON: American Chemical Society, 2012, vol. 3, No 15, p. 2087–2091. ISSN 1948-7185. Available from: https://dx.doi.org/10.1021/jz300805b.

VÁCHA, Robert, Noah S BIELER, Tuomas P J KNOWLES and Daan FRENKEL. Morphology and Kinetics of Self-assembled Peptide Aggregates Using Coarse Grained Simulations. In Gordon Research Coneference - Peptides, Chemistry and Biology of. 2012.

VÁCHA, Robert, F.J. MARTINEZ-VERACOECHEA and D. FRENKEL. Receptor-mediated endocytosis of nanoparticles of various shapes. In Biomembrane days. 2012.

VÁCHA, Robert, N.S. BIELER, T.P.J. KNOWLES and D FRENKEL. Self-Assembly of Patchy Spherocylinders. In CECAM workshop - Design of self-assembling materials. 2012.

VÁCHA, Robert. Self-assembly of Proteins and Peptides in Cellular Environment. In Telluride Science Research Center workshop Protein and Peptide Interactions in Cellular Environments. 2012.

VÁCHA, Robert and Sylvie ROKE. Sodium Dodecyl Sulfate at Water-Hydrophobic Interfaces: A Simulation Study. Journal of Physical Chemistry B. WASHINGTON: AMER CHEMICAL SOC, 2012, vol. 116, No 39, p. 11936-11942. ISSN 1520-6106. Available from: https://dx.doi.org/10.1021/jp304900z.

VÁCHA, Robert, F.J. MARTINEZ-VERACOECHEA and D. FRENKEL. Receptor-Mediated Endocytosis of Nanoparticles of Various Shapes. Nano Lett. American Chemical Society, 2011, vol. 11, No 12, p. 5391–5395. ISSN 1530-6984. Available from: https://dx.doi.org/10.1021/nl2030213.

VÁCHA, Robert and D FRENKEL. Relation between Molecular Shape and the Morphology of Self-Assembling Aggregates: A Simulation Study. Biophysical Journal. Bethesda, USA: Biophysical Society, 2011, vol. 101, No 6, p. 1432-1439. ISSN 0006-3495. Available from: https://dx.doi.org/10.1016/j.bpj.2011.07.046.

VÁCHA, Robert, S W RICK, P JUNGWIRTH, A G F DE BEER, H B DE AGUIAR, J S SAMSON and S ROKE. The Orientation and Charge of Water at the Hydrophobic Oil Droplet-Water Interface. Journal of the American Chemical Society. Washington, DC., USA: American Chemical Society, 2011, vol. 133, No 26, p. 10204-10210. ISSN 0002-7863. Available from: https://dx.doi.org/10.1021/ja202081x.