Výpis publikací

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

PAJTINKA, Peter a 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, roč. 15, č. 1, s. 175-179. ISSN 1948-7185. Dostupné z: 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 a Robert VÁCHA. Computational Design of Pore-Forming Peptides with Potent Antimicrobial and Anticancer Activities. Journal of Medicinal Chemistry. Washington: American Chemical Society, 2024, roč. 67, č. 16, s. 14040-14061. ISSN 0022-2623. Dostupné z: https://dx.doi.org/10.1021/acs.jmedchem.4c00912.

BARTOŠ, Ladislav, Anant K. MENON a Robert VÁCHA. Insertases scramble lipids: Molecular simulations of MTCH2. Structure. 2024, roč. 2024, č. 32, s. 505-510. Dostupné z: https://dx.doi.org/10.1016/j.str.2024.01.012.

KHODAM HAZRATI, Mehrnoosh a Robert VÁCHA. Membrane Adsorption Enhances Translocation of Antimicrobial Peptide Buforin 2. Journal of Physical Chemistry B. WASHINGTON: American Chemical Society, 2024, roč. 128, č. 35, s. 8469-8476. ISSN 1520-6106. Dostupné z: https://dx.doi.org/10.1021/acs.jpcb.4c04338.

BLASCO, Sofia, Lukáš SUKENÍK a Robert VÁCHA. Nanoparticle induced fusion of lipid membranes. Nanoscale. CAMBRIDGE: Royal Society of Chemistry, 2024, roč. 16, č. 21, s. 10221-10229. ISSN 2040-3364. Dostupné z: https://dx.doi.org/10.1039/d4nr00591k.

BARTOŠ, Ladislav, Martina DRABINOVÁ a Robert VÁCHA. Optimizing properties of translocation-enhancing transmembrane proteins. Biophysical Journal. 2024, roč. 123, č. 10, s. 1240-1252. ISSN 0006-3495. Dostupné z: https://dx.doi.org/10.1016/j.bpj.2024.04.009.

BIRIUKOV, Denys a 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, roč. 4, č. 4, s. 302-313. Dostupné z: https://dx.doi.org/10.1021/acsphyschemau.4c00003.

BARTOŠ, Ladislav a Robert VÁCHA. Peptide translocation across asymmetric phospholipid membranes. Biophysical Journal. Cell Press, 2024, roč. 123, č. 6, s. 693-702. ISSN 0006-3495. Dostupné z: https://dx.doi.org/10.1016/j.bpj.2024.02.006.

LINHARTOVÁ, Kateřina, Francesco Luca FALGINELLA, Martin MÁTL, Marek ŠEBESTA, Robert VÁCHA a Richard ŠTEFL. Sequence and structural determinants of RNAPII CTD phase-separation and phosphorylation by CDK7. Nature Communications. Berlin: Nature Research, 2024, roč. 15, č. 1, s. 1-17. ISSN 2041-1723. Dostupné z: https://dx.doi.org/10.1038/s41467-024-53305-2.

DEB, Rahul, Ivo KABELKA, Jan PŘIBYL a 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 a Robert VÁCHA. Designing spheroidal nanoparticles to induce membrane fusion of liposomes. In EMBO Workshop Mechanisms of membrane fusion 2023. 2023.

BIRIUKOV, Denys a 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, roč. 19, č. 18, s. 6332-6341. ISSN 1549-9618. Dostupné z: https://dx.doi.org/10.1021/acs.jctc.3c00614.

SUKENÍK, Lukáš, Liya MUKHAMEDOVA, Michaela PROCHÁZKOVÁ, Karel ŠKUBNÍK, Pavel PLEVKA a 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 a Robert VÁCHA. Membrane adsorption enhances translocation of antimicrobial peptide buforin 2. In EBSA Congress 2023. 2023.

BIRIUKOV, Denys, Riopedre Fernández MIGUEL a 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 a 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 a Anant K. MENON. Phospholipids are imported into mitochondria by VDAC, a dimeric beta barrel scramblase. Nature Communications. Heidelberger: Nature Research, 2023, roč. 14, č. 1, s. 1-16. ISSN 2041-1723. Dostupné z: 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 a 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, roč. 1869, č. 2, s. 1-12. ISSN 0925-4439. Dostupné z: https://dx.doi.org/10.1016/j.bbadis.2022.166614.

VAZDAR, K., C. TEMPRA, A. OLŻYŃSKA, Denys BIRIUKOV, L. CWIKLIK a 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, roč. 127, č. 24, s. 5462-5469. ISSN 1520-6106. Dostupné z: https://dx.doi.org/10.1021/acs.jpcb.3c03207.

FALGINELLA, Francesco Luca, Marek KRAVEC, Martina DRABINOVÁ, Petra PACLÍKOVÁ, Vítězslav BRYJA a Robert VÁCHA. Binding of DEP domain to phospholipid membranes: More than just electrostatics. Biochimica et Biophysica Acta (BBA) - Biomembranes. Amsterdam: Elsevier, 2022, roč. 1864, č. 10, s. 1-12. ISSN 0005-2736. Dostupné z: https://dx.doi.org/10.1016/j.bbamem.2022.183983.

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

SUKENÍK, Lukáš, Rahul DEB a 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 a Robert VÁCHA. Magainin 2 and PGLa in Bacterial Membrane Mimics III: Membrane Fusion and Disruption. Biophysical Journal. New York, USA: Cell Press, 2022, roč. 121, č. 5, s. 852-861. ISSN 0006-3495. Dostupné z: 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 a G. PABST. Magainin 2 and PGLa in bacterial membrane mimics IV: Membrane curvature and partitioning. BIOPHYSICAL JOURNAL. UNITED STATES: CELL PRESS, 2022, roč. 121, č. 23, s. 4689-4701. ISSN 0006-3495. Dostupné z: https://dx.doi.org/10.1016/j.bpj.2022.10.018.

PETERKOVÁ, Kateřina, Ivo DURNÍK, Radek MAREK, Janez PLAVEC a 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 a 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 a 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, roč. 65, č. 7, s. 5701-5723. ISSN 0022-2623. Dostupné z: https://dx.doi.org/10.1021/acs.jmedchem.1c02228.

DRABINOVÁ, Martina, Martina ČARNECKÁ, Otakar HUMPA, Iva SLANINOVÁ a Jiří SLANINA. Acetylace 7-hydroxy skupiny dibenzocyklooktadienových lignanů zvyšuje inhibici P-glykoproteinu. In 65. Studentská vědecká konference - program a sborník abstraktů. 2021. ISBN 978-80-210-6313-6.

KABELKA, Ivo a Robert VÁCHA. Advances in Molecular Understanding of α-helical Membrane-Active Peptides. Accounts of chemical research. American Chemical Society, 2021, roč. 54, č. 9, s. 2196-2204. ISSN 0001-4842. Dostupné z: 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 a Pavel PLEVKA. Capsid opening enables genome release of iflaviruses. Science advances. New York: American Association for the Advancement of Science, 2021, roč. 7, č. 1, s. 1-9. ISSN 2375-2548. Dostupné z: https://dx.doi.org/10.1126/sciadv.abd7130.

PROCHÁZKOVÁ, Michaela, Tibor FÜZIK, Danyil GRYBCHUK, Francesco Luca FALGINELLA, Lucie PODEŠVOVÁ, Vyacheslav YURCHENKO, Robert VÁCHA a Pavel PLEVKA. Capsid Structure of Leishmania RNA Virus 1. Journal of Virology. American Society for Microbiology, 2021, roč. 95, č. 3, s. "e01957", 12 s. ISSN 0022-538X. Dostupné z: https://dx.doi.org/10.1128/JVI.01957-20.

LABAJOVA, N., N. BARANOVA, Miroslav JURÁSEK, Robert VÁCHA, M. LOOSE a I. BARAK. Cardiolipin-Containing Lipid Membranes Attract the Bacterial Cell Division Protein DivIVA. International Journal of Molecular Sciences. Basel: Multidisciplinary Digital Publishing Institute, 2021, roč. 22, č. 15, s. 8350-8370. ISSN 1422-0067. Dostupné z: https://dx.doi.org/10.3390/ijms22158350.

SUKENÍK, Lukáš, Liya MUKHAMEDOVA, Michaela PROCHÁZKOVÁ, Karel ŠKUBNÍK, Pavel PLEVKA a 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, roč. 15, č. 12, s. 19233-19243. ISSN 1936-0851. Dostupné z: https://dx.doi.org/10.1021/acsnano.1c04814.

BARTOŠ, Ladislav, Ivo KABELKA a Robert VÁCHA. Enhanced translocation of amphiphilic peptides across membranes by transmembrane proteins. Biophysical Journal. New York, USA: Cell Press, 2021, roč. 120, č. 11, s. 2296-2305. ISSN 0006-3495. Dostupné z: 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 a Sonia GARCIA. Extraordinary diversity of telomeres, telomerase RNAs and their template regions in Saccharomycetaceae. Scientific Reports. Nature Research, 2021, roč. 11, č. 1, s. "12784", 11 s. ISSN 2045-2322. Dostupné z: https://dx.doi.org/10.1038/s41598-021-92126-x.

SAVENKO, M., Timothée Emmanuel J. RIVEL, S. YESYLEVSKYY a 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, roč. 125, č. 29, s. 8060-8074. ISSN 1520-6106. Dostupné z: https://dx.doi.org/10.1021/acs.jpcb.1c04615.

JURÁSEK, Miroslav, Jitender KUMAR, Petra PACLÍKOVÁ, Alka Kumari JADAUN, Konstantinos TRIPSIANES, Vítězslav BRYJA a Robert VÁCHA. Phosphorylation-induced changes in the PDZ domain of Dishevelled 3. Scientific Reports. NATURE PUBLISHING GROUP, 2021, roč. 11, č. 1, s. "1484", 14 s. ISSN 2045-2322. Dostupné z: https://dx.doi.org/10.1038/s41598-020-79398-5.

KABELKA, Ivo, Radim BROŽEK a Robert VÁCHA. Selecting Collective Variables and Free Energy Methods for Peptide Translocation Across Membranes. Journal of Chemical Information and Modeling. USA, 2021, roč. 61, č. 2, s. 819-830. ISSN 1549-9596. Dostupné z: 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 a R. ŠACHL. The impact of the glycan headgroup on the nanoscopic segregation of gangliosides. Biophysical Journal. New York, USA: Cell Press, 2021, roč. 120, č. 24, s. 5530-5543. ISSN 0006-3495. Dostupné z: https://dx.doi.org/10.1016/j.bpj.2021.11.017.

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

BROŽEK, Radim, Ivo KABELKA a 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, roč. 124, č. 28, s. 5940-5947. ISSN 1520-6106. Dostupné z: https://dx.doi.org/10.1021/acs.jpcb.0c03291.

JURÁSEK, Miroslav, Klas FLÄRDH a Robert VÁCHA. Effect of membrane composition on DivIVA-membrane interaction. BBA Biomembranes. Amsterdam: Elsevier, 2020, roč. 1862, č. 8, s. 1-9. ISSN 0005-2736. Dostupné z: 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 a Jozef HRITZ. Choice of Force Field for Proteins Containing Structured and Intrinsically Disordered Regions. Biophysical Journal. Bethesda, USA: Biophysical Society, 2020, roč. 118, č. 7, s. 1621-1633. ISSN 0006-3495. Dostupné z: https://dx.doi.org/10.1016/j.bpj.2020.02.019.

KABELKA, Ivo, Michael PACHLER, Sylvain PRÉVOST, Ilse LETOFSKY-PAPST, Karl LOHNER, Georg PABST a Robert VÁCHA. Magainin 2 and PGLa in Bacterial Membrane Mimics II: Membrane Fusion and Sponge Phase Formation. Biophysical Journal. Cambridge, USA: Cell Press, 2020, roč. 118, č. 3, s. 612-623. ISSN 0006-3495. Dostupné z: https://dx.doi.org/10.1016/j.bpj.2019.12.019.

FATAFTA, H., C. POOJARI, A. SAYYED-AHMAD, B. STRODEL a 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, roč. 11, č. 4, s. 535-548, 27 s. ISSN 1948-7193. Dostupné z: https://dx.doi.org/10.1021/acschemneuro.9b00558.

TÜRKOVÁ, Alžběta, Ivo KABELKA, Lukáš SUKENÍK, Šárka POKORNÁ, Martin Peter HOF a 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 a Richard ŠTEFL. Yeast Spt6 Reads Multiple Phosphorylation Patterns of RNA Polymerase II C-Terminal Domain In Vitro. Journal of Molecular Biology. Academic Press, 2020, roč. 432, č. 14, s. 4092-4107. ISSN 0022-2836. Dostupné z: 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 a 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, roč. 10, APR 18 2019, s. 1-18. ISSN 2041-1723. Dostupné z: 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 a B. STRODEL. Effects of in vivo conditions on amyloid aggregation. Chemical Society Reviews. Cambridge: RSC Publishing, 2019, roč. 48, č. 14, s. 3946-3996. ISSN 0306-0012. Dostupné z: https://dx.doi.org/10.1039/c8cs00034d.

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

OWEN, Michael Christopher, Andreas KARNER, Radek ŠACHL, Johannes PREINER, Mariana AMARO a 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, roč. 123, č. 35, s. 7504-7517. ISSN 1520-6106. Dostupné z: https://dx.doi.org/10.1021/acs.jpcb.9b05095.

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

PACHLER, Michael, Ivo KABELKA, Marie-Sousai APPAVOU, Karl LOHNER, Robert VÁCHA a Georg PABST. Magainin 2 and PGLa in Bacterial Membrane Mimics I: Peptide-Peptide and Lipid-Peptide Interactions. Biophysical Journal. New York: Cell Press, 2019, roč. 117, č. 10, s. 1858-1869. ISSN 0006-3495. Dostupné z: 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 a 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, roč. 80, JUN, s. 259-269. ISSN 1476-9271. Dostupné z: https://dx.doi.org/10.1016/j.compbiolchem.2019.04.005.

PAVLÍKOVÁ PŘECECHTĚLOVÁ, Jana, Arnošt MLÁDEK, Vojtěch ZAPLETAL a 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, roč. 15, č. 10, s. 5642-5658. ISSN 1549-9618. Dostupné z: https://dx.doi.org/10.1021/acs.jctc.8b00257.

PACHLER, M., Ivo KABELKA, R. LEBER, I. LETOFSKY-PAPST, K. LOHNER, Robert VÁCHA a 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. Dostupné z: https://dx.doi.org/10.1016/j.bpj.2018.11.280.

VÁCHA, Robert. Toxicita a aktivita antimikrobiálních peptidů. Masarykova univerzita, 2019.

LIAO, Q.H., Michael Christopher OWEN, S. BALI, B. BARZ a 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, roč. 54, č. 56, s. 7766-7769. ISSN 1359-7345. Dostupné z: https://dx.doi.org/10.1039/c8cc02263a.

TESEI, Giulio, Erik HELLSTRAND, Kalyani SANAGAVARAPU, Sara LINSE, Emma SPARR, Robert VÁCHA a 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, roč. 34, č. 4, s. 1266-1273. ISSN 0743-7463. Dostupné z: https://dx.doi.org/10.1021/acs.langmuir.7b03155.

ŠTĚPÁN, Jakub, Ivo KABELKA, Jaroslav KOČA a Petr KULHÁNEK. Behavior of BsoBI endonuclease in the presence and absence of DNA. Journal of Molecular Modeling. New York: Springer, 2018, roč. 24, č. 1, s. 22-31. ISSN 1610-2940. Dostupné z: https://dx.doi.org/10.1007/s00894-017-3557-8.

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

OWEN, Michael Christopher, W. KULIG, T. ROG, I. VATTULAINEN a 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, roč. 251, č. 3, s. 521-534. ISSN 0022-2631. Dostupné z: https://dx.doi.org/10.1007/s00232-018-0028-9.

TUBIANA, L., Miroslav JURÁSEK a I. COLUZZA. Implementing efficient concerted rotations using Mathematica and C code. EUROPEAN PHYSICAL JOURNAL E. NEW YORK: SPRINGER, 2018, roč. 41, č. 7, s. 87-95. ISSN 1292-8941. Dostupné z: https://dx.doi.org/10.1140/epje/i2018-11694-7.

KABELKA, Ivo a Robert VÁCHA. Optimal Hydrophobicity and Reorientation of Amphiphilic Peptides Translocating through Membrane. Biophysical Journal. New York, USA: Cell Press, 2018, roč. 115, č. 6, s. 1045-1054. ISSN 0006-3495. Dostupné z: 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 a Lydie IZAKOVIČOVÁ HOLLÁ. Personalizovaná terapie pacientů s gastroezofageální refluxní chorobou - metodika stanovení genového profilu CYP2C19. Gastroenterologie a Hepatologie. Praha: Ambit Media, 2018, roč. 72, č. 4, s. 320-328. ISSN 1804-7874. Dostupné z: https://dx.doi.org/10.14735/amgh2018320.

OWEN, Michael Christopher, W. KULIG, C. POOJARI, T. ROG a 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, roč. 1860, č. 9, s. 1709-1720. ISSN 0005-2736. Dostupné z: 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 a G. PABST. Synergism of Antimicrobial Frog Peptides Couples to Membrane Intrinsic Curvature Strain. Biophysical Journal. New York, USA: Cell Press, 2018, roč. 114, č. 8, s. 1945-1954. ISSN 0006-3495. Dostupné z: https://dx.doi.org/10.1016/j.bpj.2018.03.006.

ZAPLETAL, Vojtěch, Arnošt MLÁDEK, Jozef HRITZ a 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 a Robert VÁCHA. Design of Multivalent Inhibitors for Preventing Cellular Uptake. Scientific Reports. London: Nature Publishing Group, 2017, roč. 7, SEP, s. 11689-11695. ISSN 2045-2322. Dostupné z: 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 a 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, roč. 89, s. 58-72. Dostupné z: https://dx.doi.org/10.1111/tpj.13322.

JURÁSEK, Miroslav a Robert VÁCHA. Self-assembled clusters of patchy rod-like molecules. SOFT MATTER. CAMBRIDGE: ROYAL SOC CHEMISTRY, 2017, roč. 13, č. 41, s. 7492-7497. ISSN 1744-683X. Dostupné z: 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 a Martin HOF. (GM1) Ganglioside Inhibits beta-Amyloid Oligomerization Induced bySphingomyelin. Angewandte Chemie International Edition. WEINHEIM: Wiley-V C H VERLAG GMBH, 2016, roč. 55, č. 32, s. 9411-9415. ISSN 1433-7851. Dostupné z: 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 a 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 a Robert VÁCHA. Influence of ligand distribution on uptake efficiency. SOFT MATTER. CAMBRIDGE: ROYAL SOC CHEMISTRY, 2015, roč. 11, č. 14, s. 2726-2730. ISSN 1744-683X. Dostupné z: https://dx.doi.org/10.1039/c4sm02815e.

KABELKA, Ivo a Robert VÁCHA. Optimal conditions for opening of membrane pore by amphiphilic peptides. JOURNAL OF CHEMICAL PHYSICS. Melville (USA): AMER INST PHYSICS, 2015, roč. 143, č. 24, s. nestránkováno, 6 s. ISSN 0021-9606. Dostupné z: https://dx.doi.org/10.1063/1.4933229.

KRUSE, Holger, Arnošt MLÁDEK, Konstantinos GKIONIS, Andreas HANSEN, Sstefan GRIMME a 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, roč. 11, č. 10, s. 4972-4991. ISSN 1549-9618. Dostupné z: 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 a D FRENKEL. Double-belt a Novel Structure of Membrane Pore. In 4th International Meeting on Antimicrobial Peptides (IMAP). 2014.

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

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

VÁCHA, Robert, Frank UHLIG a 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, s. 69-95. Volume 155. ISBN 978-1-118-75577-8. Dostupné z: https://dx.doi.org/10.1002/9781118755815.ch02.

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

VÁCHA, Robert a D. FRENKEL. Simulations Suggest Possible Novel Membrane Pore Structure. Langmuir. Washington D.C.: Amer Chemical Soc, 2014, roč. 30, č. 5, s. 1304-1310. ISSN 0743-7463. Dostupné z: https://dx.doi.org/10.1021/la402727a.

VÁCHA, Robert a D. FRENKEL. Stability of Bicelles: A Simulation Study. Langmuir. WASHINGTON: AMER CHEMICAL SOC, 1155 16TH ST, NW, WASHINGTON, DC 20036 USA, 2014, roč. 30, č. 15, s. 4229-4235. ISSN 0743-7463. Dostupné z: https://dx.doi.org/10.1021/la4048159.

VÁCHA, Robert, S. LINSE a M. LUND. Surface Effects on Aggregation Kinetics of Amyloidogenic Peptides. Journal of the American Chemical Society. Washington, D.C.: American Chemical Society, 2014, roč. 136, č. 33, s. 11776-11782. ISSN 0002-7863. Dostupné z: https://dx.doi.org/10.1021/ja505502e.

VÁCHA, Robert, S LINSE a 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 a 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 a 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, roč. 135, č. 40, s. 15263-15268. ISSN 0002-7863. Dostupné z: https://dx.doi.org/10.1021/ja408582w.

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

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

BERKOWITZ, M. L. a Robert VÁCHA. Aqueous Solutions at the Interface with Phospholipid Bilayers. Accounts of chemical research. Washington: American Chemical Society, 2012, roč. 45, č. 1, s. 74-82. ISSN 0001-4842. Dostupné z: https://dx.doi.org/10.1021/ar200079x.

BIELER, Noah S., Tuomas P.J. KNOWLES, Daan FRENKEL a Robert VÁCHA. Connecting Macroscopic Observables and Microscopic Assembly Events in Amyloid Formation Using Coarse Grained Simulations. PLOS Computational Biology. San Francisco: PLOS, 2012, roč. 8, č. 10, s. "nestránkováno", 10 s. ISSN 1553-7358. Dostupné z: https://dx.doi.org/10.1371/journal.pcbi.1002692.

VÁCHA, Robert, Ondrej MARSALEK, A.P. WILLARD, D.J. BONTHUIS, R.R. NETZ a 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, roč. 3, č. 1, s. 107–111. ISSN 1948-7185. Dostupné z: https://dx.doi.org/10.1021/jz20148521.

VÁCHA, Robert, Francisco J. MARTINEZ-VERACOECHEA a Daan FRENKEL. Intracellular Release of Endocytosed Nanoparticles Upon a Change of Ligand-Receptor Interaction. ACS Nano. WASHINGTON: American Chemical Society, 2012, roč. 6, č. 12, s. 10598-10605. ISSN 1936-0851. Dostupné z: https://dx.doi.org/10.1021/nn303508c.

VAZDAR, Mario, Eva PLUHAŘOVÁ, Phil E MASON, Robert VÁCHA a Pavel JUNGWIRTH. Ions at Hydrophobic Aqueous Interfaces: Molecular Dynamics with Effective Polarization. Journal of Physical Chemistry Letters. WASHINGTON: American Chemical Society, 2012, roč. 3, č. 15, s. 2087–2091. ISSN 1948-7185. Dostupné z: https://dx.doi.org/10.1021/jz300805b.

VÁCHA, Robert, Noah S BIELER, Tuomas P J KNOWLES a 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 a D. FRENKEL. Receptor-mediated endocytosis of nanoparticles of various shapes. In Biomembrane days. 2012.

VÁCHA, Robert, N.S. BIELER, T.P.J. KNOWLES a 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 a Sylvie ROKE. Sodium Dodecyl Sulfate at Water-Hydrophobic Interfaces: A Simulation Study. Journal of Physical Chemistry B. WASHINGTON: AMER CHEMICAL SOC, 2012, roč. 116, č. 39, s. 11936-11942. ISSN 1520-6106. Dostupné z: https://dx.doi.org/10.1021/jp304900z.

VÁCHA, Robert, F.J. MARTINEZ-VERACOECHEA a D. FRENKEL. Receptor-Mediated Endocytosis of Nanoparticles of Various Shapes. Nano Lett. American Chemical Society, 2011, roč. 11, č. 12, s. 5391–5395. ISSN 1530-6984. Dostupné z: https://dx.doi.org/10.1021/nl2030213.

VÁCHA, Robert a D FRENKEL. Relation between Molecular Shape and the Morphology of Self-Assembling Aggregates: A Simulation Study. Biophysical Journal. Bethesda, USA: Biophysical Society, 2011, roč. 101, č. 6, s. 1432-1439. ISSN 0006-3495. Dostupné z: 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 a 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, roč. 133, č. 26, s. 10204-10210. ISSN 0002-7863. Dostupné z: https://dx.doi.org/10.1021/ja202081x.