Biomolecular Modelling Group

 
We are a theoretical group located at the Centre of New Technolgies (CeNT), University of Warsaw, Poland.
We apply physical models to describe and simulate biological molecules in order to gain insight into principles governing their structure, dynamics and function.
We are particularly interested in the interplay between the molecules themselves and aqueous environment they live in. To this end, we are studying conformation dependent protein hydration free energies, investigate the role buried water molecules, and develop new theoretical approaches to describe macromolecular hydration.
Piotr Setny, PhD, DSc
email: p.setny@cent.uw.edu.pl
phone: +48 22 55 43660
room: 04.06
www: http://setnylab.cent.uw.edu.pl

Research interests
Piotr Setny is a theoretical and computational biophysicist. He develops and applies physical models to describe and simulate biological molecules in order to gain insight into principles governing their structure, dynamics and function. He is particularly interested in the interplay between the molecules themselves and aqueous environment they live in. To this end, he is studying conformation dependent protein hydration free energies, investigate the role buried water molecules, and develop new theoretical approaches to describe macromolecular hydration. One of his new recent research topics is behaviour of polypeptides and proteins at the interface between aqueous solution and lipid membranes

Education and degrees:
2008 PhD, with honours, Physics Department, University of Warsaw, Poland
2003 MSc, summa cum laude, Physics Department, University of Warsaw, Poland
2001 MD, Medical University of Warsaw, Poland

Positions:
2017 – group leader at CeNT
2013 – 2017 independent researcher, CeNT
2009 -2013 postdoctoral researcher, Physics Department, Technical University of Munich, Germany (the group of Prof. Martin Zacharias)
2009 visiting scholar, Department of Chemistry and Biochemistry and Center for Theoretical Biological Physics, University of California, San Diego, USA (the group of Prof. J. Andrew McCammon)

Selected publications:
• Piotr Setny, Marta D. Wiśniewska, Water-mediated conformational preselection mechanism in substrate binding cooperativity to protein kinase A, PNAS, 115:3852, 2018
• Piotr Setny, Anita Dudek, Explicit Solvent Hydration Benchmark for Proteins With Application to the PBSA Method, JCTC, 13:2762, 201
• 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
• Piotr Setny, Prediction of water binding to protein hydration sites with discrete, semi-explicit solvent model, JCTC, 11:5961, 2015
• Piotr Setny, Hydration in Discrete Water (II): From Neutral to Charged Solutes, J. Phys Chem. B, 119:5970, 2015
• Piotr Setny, and M. Zacharias, Elastic network models of nucleic acids flexibility, JCTC, 9:5460, 2013
• 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
• Piotr Setny and Martin Zacharias, A coarse-grained force field for Protein-RNA docking, Nucleic Acids Res., 39: 9118, 2011
• Riccardo Baron, Piotr Setny, and J. Andrew McCammon, Water in Cavity-Ligand Recognition, J. Am. Chem. Soc., 132: 12091, 2010


Group Leader:
Piotr Setny, PhD, DSc


Postdoctoral Fellow:
Jan Stępień, PhD

PhD students:
Maria Domańska, MSc
Michał Michalski, MSc , mgr

Students:

Julia Szkóp

Jan Malinowski


Alumni:
Marta D. Wiśniewska
Marcin Sobieraj, PhD
Anita Dudek, MSc
Granger Causality Analysis of Chignolin Folding
Marcin Sobieraj, Piotr Setny
J. Chem. Theory Comput. 2022, 18, 3, 1936–1944
Transient Excursions to Membrane Core as Determinants of Influenza Virus Fusion Peptide Activity
Remigiusz Worch, Anita Dudek, Paulina Borkowska, Piotr Setny
Int J Mol Sci., 22:5301
Entropy-based distance cutoff for protein internal contact networks
Marcin Sobieraj, Piotr Setny
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 89:1333
GridSolvate: A Web Server for the Prediction of Biomolecular Hydration Properties
Setny, P.
Journal of chemical information and modeling
Conserved internal hydration motifs in protein kinases
Setny, P.
Proteins: Structure, Function, and Bioinformatics, 88(12), 1578-1591
Water-mediated conformational preselection mechanism in substrate binding cooperativity to protein kinase A
Setny, P., & Wiśniewska, M. D. (2018).
A. Proceedings of the National Academy of Sciences, 115(15), 3852-3857
Charged N-terminus of Influenza Fusion Peptide Facilitates Membrane Fusion
Worch, R., Dudek, A., Krupa, J., Szymaniec, A., & Setny, P. (2018).
International journal of molecular sciences, 19(2), 578
Water-mediated conformational preselection mechanism in substrate binding cooperativity to protein kinase A
Setny, P., & Wiśniewska, M. D. (2018).
Proceedings of the National Academy of Sciences, 115(15), 3852-3857.
Affinity, kinetics, and pathways of anisotropic ligands binding to hydrophobic model pockets
Weiß, R. G., Chudoba, R., Setny, P., & Dzubiella, J.
The Journal of Chemical Physics, 149(9)
Three conserved C-terminal residues of influenza fusion peptide alter its behavior at the membrane interface.
Worch, R., Krupa, J., Filipek, A., Szymaniec, A., & Setny, P. (2017).
Biochimica et Biophysica Acta (BBA)-General Subjects, 1861(2), 97-105.
Explicit Solvent Hydration Benchmark for Proteins with Application to the PBSA Method
Setny, P., & Dudek, A. (2017).
Journal of chemical theory and computation, 13(6), 2762-2776.
Principles for Tuning Hydrophobic Ligand–Receptor Binding Kinetics
Weiß, R. G., Setny, P., & Dzubiella, J. (2017).
Journal of chemical theory and computation, 13(6), 3012-3019.
Computational study on donor–acceptor optical markers for Alzheimer’s disease: a game of charge transfer and electron delocalization.
Peccati, F., Wiśniewska, M., Solans-Monfort, X., & Sodupe, M. (2016).
Physical Chemistry Chemical Physics, 18(17), 11634-11643.
Structural and energetic comparison of the complexes of aminoglycosides with the model of the ribosomal A-site.
Kulik, M., & Trylska, J. (2016).
RAIRO-Operations Research, 50(2), 375-386.
Solvent Fluctuations Induce Non-Markovian Kinetics in Hydrophobic Pocket-Ligand Binding
Weiß, R. G., Setny, P., & Dzubiella, J. (2016).
The Journal of Physical Chemistry B, 120(33), 8127-8136.
Hydration in Discrete Water (II): From Neutral to Charged Solutes.
Setny, P. (2015).
The Journal of Physical Chemistry B, 119(19), 5970-5978.
Hydratation in Discrete Water (II): From neutral to charged solutes
Setny, P. (2015)
The Journal of Physical Chemistry B, 119(19), 5970-5978.
Elastic network models of nucleic acids flexibility.
Setny, P., & Zacharias, M. (2013).
Journal of chemical theory and computation, 9(12), 5460-5470.