Publications

  • Paulina Szymczak, Marcin Możejko, Tomasz Grzegorzek, Radosław Jurczak, Marta Bauer, Damian Neubauer, Karol Sikora, Michał Michalski, Jacek Sroka, Piotr Setny, Wojciech Kamysz,  and Ewa Szczurek Discovering highly potent antimicrobial peptides with deep generative model HydrAMP, Nat. Commun. 14: 1453, 2023 (link)
  • Michał Michalski and Piotr Setny, Membrane-Bound Configuration and Lipid Perturbing Effects of Hemagglutinin Subunit 2 N-Terminus Investigated by Computer Simulations, Front. Mol. Biosci., 9:1–14, 2022 (link)
  • Adam Stasiulewicz, Anna Lesniak, Piotr Setny, Magdalena Bujalska-Zadrożny, and Joanna I. Sulkowska Identification of CB1 Ligands among Drugs, Phytochemicals and Natural-Like Compounds: Virtual Screening and In Vitro Verification, ACS Chem. Neurosci. 13:2991, 2022 (link)
  • Marcin Sobieraj and P. Setny, Granger Causality Analysis of Chignolin Folding, J. Chem. Theory Comput., 18:1936, 2022 (link)
  • Marcin Sobieraj and Piotr Setny, Entropy‐based distance cutoff for protein internal contact networks,  Proteins Struct. Funct. Bioinforma., 89:1333, 2021 (link)
  • Remigiusz Worch, Anita Dudek, Paulina Borkowska, and Piotr Setny, Transient Excursionsto Membrane Core as Determinants of Influenza Virus Fusion Peptide Activity, Int. J. Mol. Sci.,  22:5301, 2021 (link)
  • Piotr Setny, GridSolvate: a web server for the prediction of biomolecular hydration properties, J. Chem. Inf. Model.  60: 5908, 2020  (link)
  • Piotr Setny, Conserved internal hydration motifs in protein kinases, Proteins 88:1578, 2020 (link)
  • Agata Perlińska, Adam Stasiulewicz, Ewa Nawrocka,  Krzysztof Kazimierczuk, Piotr Setny, Joanna Sułkowska, Restriction of S-adenosylmethionine conformational freedom by knotted protein binding sites, Plos Comp. Biol., 16:e1007904, 2020  (link)
  • Małgorzata Rytel, Paweł Kasprzak, Piotr Setny, Krzysztof Kazimierczuk, Quick temperature-sweep pure-shift NMR: the case of solvent effects in atorvastatin, PCCP, 21:19209, 2019 (link)
  • Gregor Weiss, Richard Chudoba, Piotr Setny, Joachim Dzubiella,  Affinity, kinetics, and pathways of anisotropic ligands binding to hydrophobic model pockets, J. Chem. Phys, 149:94902, 2018 (link)
  • Piotr Setny, Marta D. Wiśniewska, Water-mediated conformational preselection mechanism in substrate binding cooperativity to protein kinase A, PNAS, 115:3852, 2018 (link)
  • Remigiusz Worch, Anita Dudek, Joanna Krupa, Anna Szymaniec, Piotr Setny,  Charged n-terminus of influenza fusion peptide facilitates membrane fusion, Int. J. Mol. Sci., 19:578, 2018 (link)
  • Piotr Setny, Anita Dudek, Explicit Solvent Hydration Benchmark for Proteins With Application to the PBSA Method, JCTC, 13:2762, 2017 (link)
  • Gregor Weiss, Piotr Setny, Joachim Dzubiella, Principles for Tuning Hydrophobic Ligand-Receptor Binding Kinetics, JCTC, 13:3012, 2017 (link)
  • Remigiusz Worch, Joanna Krupa, Alicja Filipek, Anna Szymaniec, Piotr Setny,\ Three conserved C-terminal residues of influenza fusion peptide alter its behavior at the membrane interface, BBA-GEN Subjects, 2:97, 2017 (link)
  • Gregor Weiss, Piotr Setny, and Joachim Dzubiella, Solvent Fluctuations Induce Non-Markovian Kinetics in Hydrophobic Pocket-Ligand Binding, J. Phys. Chem. B, 120:8127, 2016 (link)
  • Piotr Setny, Prediction of water binding to protein hydration sites with discrete, semi-explicit solvent model, JCTC, 11:5961, 2015 (link)
  • Piotr Setny, Hydration in Discrete Water (II): From Neutral to Charged Solutes, J. Phys Chem. B, 119:5970, 2015 (link)
  • Piotr Setny, and M. Zacharias, Elastic network models of nucleic acids flexibility, JCTC, 9:5460, 2013 (link)
  • B. Steuten, Piotr Setny, M. Zacharias, and R. Wagner, Mapping the spatial neighbourhood of the regulatory 6S RNA bound to Escherichia coli RNA polymerase holoenzyme. J. Mol. Biol,, 425:3649, 2013 (link)
  • Piotr Setny, Peter Kekenes-Huskey, Riccardo Baron, J. Andrew McCammon, and Joachim Dzubiella, Solvent fluctuations in hydrophobic cavity-ligand binding kinetics, Proc. Natl. Acad. Sci. U.S.A., 110:1194, 2013 (link)
  • Piotr Setny, Riccardo Baron, and J. Andrew McCammon, Comment on \”Molecular driving forces of the pocket-ligand hydrophobic association\” by G. Graziano Chem. Phys. Lett. 95:533, 2012 Chem. Phys. Lett. , 55:306, 2013 (link)
  • Riccardo Baron, Piotr Setny, and Francesco Pesani, Water Structure, Dynamics, and Spectral Signatures: Changes Upon Model Cavity-Ligand Recognition,  J. Phys. Chem. B , 46:13774, 2012 (link)
  • Piotr Setny, Ranjit P. Bahadur, and Martin Zacharias, Protein-DNA docking with a coarse-grained force field, BMC Bioinformatics, 13:228, 2012 (link)
  • Riccardo Baron, Piotr Setny, and J. Andrew McCammon, Hydrophobic Association and Volume-Confined Water Molecules, Methods & Principles in Med. Chem. – Protein-Ligand Interactions. , Gohlke H (Ed.), Wiley-VCH, 2012 (link)
  • Piotr Setny and Martin Zacharias, A coarse-grained force field for Protein-RNA docking, Nucleic Acids Res., 39: 9118, 2011 (link)
  • Piotr Setny and Martin Zacharias, Hydration in Discrete Water. A Mean Field, Cellular Automata Based Approach to Calculating Hydration Free Energies, J. Phys. Chem. B., 114: 8667, 2010 (link)
  • Riccardo Baron, Piotr Setny, and J. Andrew McCammon, Water in Cavity-Ligand Recognition, J. Am. Chem. Soc., 132: 12091, 2010 (link)
  • Piotr Setny, Riccardo Baron, and J. Andrew McCammon, How Can Hydrophobic Association Be Enthalpy Driven?, J. Chem. Theory and Comp., 6: 2866, 2010 (link)
  • Piotr Setny, Zhongming Wang, Li-Tien Cheng, Bo Li, J. Andrew McCammon, and Joachim Dzubiella, Dewetting-Controlled Binding of Ligands to Hydrophobic Pockets, Phys. Rev. Lett., 131: 144102, 2009 (link)
  • Li-Tien Cheng, Zhongming Wang, Piotr Setny, Joachim Dzubiella, Bo Li, and J. Andrew McCammon,\ Interfaces and hydrophobic interactions in receptor-ligand systems: A level-set variational implicit solvent approach, J. Chem. Phys., 131: 144102, 2009 (link)
  • Piotr Setny and Joanna Trylska, Search for Novel Aminoglycoside Derivatives by Combining Fragment-based Virtual Screening and 3D-QSAR Scoring,  J. Chem. Inf. Model., 49: 390, 2009 (link)
  • Julia Romanowska, Piotr Setny, and Joanna Trylska, Molecular dynamics study of the ribosomal A-site,\ J. Phys. Chem. B., 112: 15227, 2008 (link)
  • Piotr Setny, Hydrophobic interactions between methane and a nanoscopic pocket: Three dimensional distribution of potential of mean force revealed by computer simulations, J. Chem. Phys., 128: 125105, 2008 (link)
  • Piotr Setny, Water properties and potential of mean force for hydrophobic interactions of methane and nanoscopic pockets studied by computer simulations,  J. Chem. Phys., 127: 054505, 2007 (link)
  • Piotr Setny, Bogdan Lesyng, and Waldemar Priebe, Modelling of possible binding modes of caffeic acid derivatives to jak2 kinase, Acta Biochim. Pol., 54: 64, 2007 (link)
  • Piotr Setny and Maciej Geller Water properties inside nanoscopic hydrophobic pocket studied by computer simulations, J. Chem. Phys., 125: 14417, 2006 (link)
  • Piotr Setny and Maciej Geller, Refinement of X-ray data on dual cosubstrate specificity of CK2 kinase by free energy calculations based on molecular dynamics simulation, Proteins, 58: 511, 2005 (link)
Scroll to Top