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Improvements and new functionalities of UNRES server for coarse-grained modeling of protein structure, dynamics, and interactions
Abstract
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.
Citations
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Authors (4)
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Cezary Czaplewski Dr hab.
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Adam Liwo
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Full text
- Publication version
- Accepted or Published Version
- DOI:
- Digital Object Identifier (open in new tab) 10.3389/fmolb.2022.1071428
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Details
- Category:
- Articles
- Type:
- artykuły w czasopismach
- Published in:
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Frontiers in Molecular Biosciences
no. 14,
ISSN: - Language:
- English
- Publication year:
- 2022
- Bibliographic description:
- Ślusarz R., Lubecka E., Czaplewski C., Liwo A.: Improvements and new functionalities of UNRES server for coarse-grained modeling of protein structure, dynamics, and interactions// Frontiers in Molecular Biosciences -Vol. 14,iss. 9 (2022),
- DOI:
- Digital Object Identifier (open in new tab) 10.3389/fmolb.2022.1071428
- Sources of funding:
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- Free publication
- Verified by:
- Gdańsk University of Technology
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