UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics

Cezary Czaplewski , Agnieszka Karczyńska , Adam Sieradzan , Józef Adam Liwo

Abstract

A server implementation of the UNRES package ( http://www.unres.pl ) for coarse-grained simulations of protein structures with the physics-based UN- RES model, coined a name UNRES server, is pre- sented. In contrast to most of the protein coarse- grained models, owing to its physics-based origin, the UNRES force field can be used in simulations, including those aimed at protein-structure predic- tion, without ancillary information from structural databases; however, the implementation includes the possibility of using restraints. Local energy mini- mization, canonical molecular dynamics simulations, replica exchange and multiplexed replica exchange molecular dynamics simulations can be run with the current UNRES server; the latter are suitable for protein-structure prediction. The user-supplied input includes protein sequence and, optionally, restraints from secondary-structure prediction or small x-ray scattering data, and simulation type and parameters which are selected or typed in. Oligomeric proteins, as well as those containing D-amino-acid residues and disulfide links can be treated. The output is dis- played graphically (minimized structures, trajecto- ries, final models, analysis of trajectory / ensembles); however, all output files can be downloaded by the user. The UNRES server can be freely accessed at http://unres-server.chem.ug.edu.pl
Author Cezary Czaplewski (FCh / DTCh / LSP)
Cezary Czaplewski,,
- Laboratory of Simulation of Polymers
, Agnieszka Karczyńska (FCh / DTCh / LMM)
Agnieszka Karczyńska,,
- Laboratory of Molecular Modeling
, Adam Sieradzan (FCh / DTCh / LMM)
Adam Sieradzan,,
- Laboratory of Molecular Modeling
, Józef Adam Liwo (FCh / DTCh / LMM)
Józef Adam Liwo,,
- Laboratory of Molecular Modeling
Journal seriesNucleic Acids Research, ISSN 0305-1048, (A 40 pkt)
Issue year2018
Vol46
NoW1
PagesW304-W309
Publication size in sheets0.5
DOIDOI:10.1093/nar/gky328
URL http://europepmc.org/articles/PMC6031057;jsessionid=CA7D2738DE2B1E274557BCBF397BC012
Languageen angielski
LicenseOther; published final; Uznanie Autorstwa - Użycie Niekomercyjne (CC-BY-NC); with publication
Score (nominal)40
ScoreMinisterial score = 40.0, 20-09-2018, ArticleFromJournal
Ministerial score (2013-2016) = 40.0, 20-09-2018, ArticleFromJournal
Publication indicators WoS Impact Factor: 2016 = 10.162 (2) - 2016=9.338 (5)
Citation count*2 (2018-11-16)
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