Department of Structural Biology, 299 Campus Dr W, Fairchild Bldg, Room D100, Stanford University, Stanford, CA 94305, USA.
Nucleic Acids Res. 2012 Jul;40(Web Server issue):W323-8. doi: 10.1093/nar/gks376. Epub 2012 May 7.
The KoBaMIN web server provides an online interface to a simple, consistent and computationally efficient protein structure refinement protocol based on minimization of a knowledge-based potential of mean force. The server can be used to refine either a single protein structure or an ensemble of proteins starting from their unrefined coordinates in PDB format. The refinement method is particularly fast and accurate due to the underlying knowledge-based potential derived from structures deposited in the PDB; as such, the energy function implicitly includes the effects of solvent and the crystal environment. Our server allows for an optional but recommended step that optimizes stereochemistry using the MESHI software. The KoBaMIN server also allows comparison of the refined structures with a provided reference structure to assess the changes brought about by the refinement protocol. The performance of KoBaMIN has been benchmarked widely on a large set of decoys, all models generated at the seventh worldwide experiments on critical assessment of techniques for protein structure prediction (CASP7) and it was also shown to produce top-ranking predictions in the refinement category at both CASP8 and CASP9, yielding consistently good results across a broad range of model quality values. The web server is fully functional and freely available at http://csb.stanford.edu/kobamin.
KoBaMIN 网页服务器提供了一个在线接口，用于一个简单、一致且计算效率高的蛋白质结构精修协议，该协议基于基于平均力势的知识库进行最小化。该服务器可用于从其未精修的 PDB 格式坐标开始，对单个蛋白质结构或蛋白质集合进行精修。由于底层知识库源自 PDB 中存储的结构，因此该精修方法特别快速和准确；因此，能量函数隐含地包含了溶剂和晶体环境的影响。我们的服务器允许使用 MESHI 软件进行可选但推荐的优化立体化学步骤。KoBaMIN 服务器还允许将精修结构与提供的参考结构进行比较，以评估精修协议带来的变化。KoBaMIN 的性能已在大量的诱饵上进行了广泛的基准测试，所有模型均在第七次蛋白质结构预测技术关键评估实验 (CASP7) 中生成，并且在 CASP8 和 CASP9 的精修类别中也产生了排名靠前的预测结果，在广泛的模型质量值范围内均能获得一致的良好结果。该网页服务器完全可用，并可在 http://csb.stanford.edu/kobamin 免费获取。
