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PREFMD: a web server for protein structure refinement via molecular dynamics simulations.

ABSTRACT:

Summary

Refinement of protein structure models is a long-standing problem in structural bioinformatics. Molecular dynamics-based methods have emerged as an avenue to achieve consistent refinement. The PREFMD web server implements an optimized protocol based on the method successfully tested in CASP11. Validation with recent CASP refinement targets shows consistent and more significant improvement in global structure accuracy over other state-of-the-art servers.

Availability and implementation

PREFMD is freely available as a web server at http://feiglab.org/prefmd. Scripts for running PREFMD as a stand-alone package are available at https://github.com/feiglab/prefmd.git.

Contact

feig@msu.edu.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Heo L

PROVIDER: S-EPMC5860225 | biostudies-literature | 2018 Mar

REPOSITORIES: biostudies-literature

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PREFMD: a web server for protein structure refinement via molecular dynamics simulations.

Heo Lim L Feig Michael M

Bioinformatics (Oxford, England) 20180301 6

<h4>Summary</h4>Refinement of protein structure models is a long-standing problem in structural bioinformatics. Molecular dynamics-based methods have emerged as an avenue to achieve consistent refinement. The PREFMD web server implements an optimized protocol based on the method successfully tested in CASP11. Validation with recent CASP refinement targets shows consistent and more significant improvement in global structure accuracy over other state-of-the-art servers.<h4>Availability and implem ...[more]

PMID: 29126101

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