Dataset Information
PREFMD: a web server for protein structure refinement via molecular dynamics simulations.
Ontology highlight
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
Publications
PREFMD: a web server for protein structure refinement via molecular dynamics simulations.
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]