Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field

Adam K Sieradzan; Cezary Czaplewski; Paweł Krupa; Magdalena A Mozolewska; Agnieszka S Karczyńska; Agnieszka G Lipska; Emilia A Lubecka; Ewa Gołaś; Tomasz Wirecki; Mariusz Makowski; Stanisław Ołdziej; Adam Liwo

doi:10.1007/978-1-0716-1716-8_23

Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field

Methods Mol Biol. 2022:2376:399-416. doi: 10.1007/978-1-0716-1716-8_23.

Affiliations

¹ Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland.
² Institute of Physics, Polish Academy of Sciences, Warsaw, Poland.
³ Institute of Computer Science, Polish Academy of Sciences, Warsaw, Poland.
⁴ Faculty of Electronics, Telecommunications and Informatics, Gdańsk University of Technology, Gdańsk, Poland.
⁵ Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.
⁶ Laboratory of Biopolymer Structure, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland.
⁷ Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland. adam.liwo@ug.edu.pl.

PMID: 34845623
DOI: 10.1007/978-1-0716-1716-8_23

Abstract

The physics-based united-residue (UNRES) model of proteins ( www.unres.pl ) has been designed to carry out large-scale simulations of protein folding. The force field has been derived and parameterized based on the principles of statistical-mechanics, which makes it independent of structural databases and applicable to treat nonstandard situations such as, proteins that contain D-amino-acid residues. Powered by Langevin dynamics and its replica-exchange extensions, UNRES has found a variety of applications, including ab initio and database-assisted protein-structure prediction, simulating protein-folding pathways, exploring protein free-energy landscapes, and solving biological problems. This chapter provides a summary of UNRES and a guide for potential users regarding the application of the UNRES package in a variety of research tasks.

Keywords: Coarse graining; Molecular dynamics simulations; Protein dynamics; Protein folding; Protein–structure prediction.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Entropy
Molecular Dynamics Simulation
Protein Conformation*
Protein Folding
Proteins

Substances

Proteins