ArticleNucleic acids research2018
UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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37 citing papers in PubMed, 79 citations in OpenAlex.
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- Secondary Structure in Free and Assisted Modeling of Proteins with the Coarse-Grained UNRES Force Field.Methods in molecular biology (Clifton, N.J.) · 2025Article
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- Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Probing Protein Aggregation Using the Coarse-Grained UNRES Force Field.Methods in molecular biology (Clifton, N.J.) · 2022Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A server implementation of the UNRES package (http://www.unres.pl) for coarse-grained simulations of protein structures with the physics-based UNRES model, coined a name UNRES server, is presented. 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 prediction, without ancillary information from structural databases; however, the implementation includes the possibility of using restraints. Local energy minimization, 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 displayed graphically (minimized structures, trajectories, 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.
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