Frontiers in Molecular Biosciences (Dec 2022)

Improvements and new functionalities of UNRES server for coarse-grained modeling of protein structure, dynamics, and interactions

  • Rafał Ślusarz,
  • Emilia A. Lubecka,
  • Cezary Czaplewski,
  • Adam Liwo

DOI
https://doi.org/10.3389/fmolb.2022.1071428
Journal volume & issue
Vol. 9

Abstract

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In this paper we report the improvements and extensions of the UNRES server (https://unres-server.chem.ug.edu.pl) for physics-based simulations with the coarse-grained UNRES model of polypeptide chains. The improvements include the replacement of the old code with the recently optimized one and adding the recent scale-consistent variant of the UNRES force field, which performs better in the modeling of proteins with the β and the α+β structures. The scope of applications of the package was extended to data-assisted simulations with restraints from nuclear magnetic resonance (NMR) and chemical crosslink mass-spectroscopy (XL-MS) measurements. NMR restraints can be input in the NMR Exchange Format (NEF), which has become a standard. Ambiguous NMR restraints are handled without expert intervention owing to a specially designed penalty function. The server can be used to run smaller jobs directly or to prepare input data to run larger production jobs by using standalone installations of UNRES.

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