Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.
Bioinformatics. 2018 Mar 15;34(6):1063-1065. doi: 10.1093/bioinformatics/btx726.
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.
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.
Supplementary data are available at Bioinformatics online.
蛋白质结构模型的精修是结构生物信息学中长期存在的问题。基于分子动力学的方法已成为实现一致精修的途径。PREFMD 网络服务器实现了一种基于在 CASP11 中成功测试的方法的优化方案。使用最近的 CASP 精修靶标进行验证表明，与其他最先进的服务器相比，该方法在全局结构准确性方面具有更一致和更显著的改进。
PREFMD 作为一个网络服务器，可在 http://feiglab.org/prefmd 上免费获得。作为独立软件包运行 PREFMD 的脚本可在 https://github.com/feiglab/prefmd.git 上获得。
补充数据可在“Bioinformatics”在线获得。
