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

Lim Heo | Zendy; Michael Feig | Zendy

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

Author(s) -

Lim Heo,

Michael Feig

Publication year - 2017

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btx726

Subject(s) - computer science , scripting language , web server , casp , software , server , web application , protocol (science) , application server , data mining , protein structure prediction , bioinformatics , programming language , the internet , protein structure , operating system , biology , medicine , alternative medicine , pathology , biochemistry

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.

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