AUTHOR=Ślusarz Rafał , Lubecka Emilia A. , Czaplewski Cezary , Liwo Adam 

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

JOURNAL=Frontiers in Molecular Biosciences

VOLUME=9

YEAR=2022

URL=https://www.frontiersin.org/journals/molecular-biosciences/articles/10.3389/fmolb.2022.1071428

DOI=10.3389/fmolb.2022.1071428

ISSN=2296-889X

ABSTRACT=<p>In this paper we report the improvements and extensions of the UNRES server (<ext-link ext-link-type="uri" xlink:href="https://unres-server.chem.ug.edu.pl" xmlns:xlink="http://www.w3.org/1999/xlink">https://unres-server.chem.ug.edu.pl</ext-link>) 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 <italic>β</italic> and the <italic>α</italic>+<italic>β</italic> 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.</p>