Department of Chemistry, Seoul National University, Seoul 151-747, Korea.
Nucleic Acids Res. 2013 Jul;41(Web Server issue):W384-8. doi: 10.1093/nar/gkt458. Epub 2013 Jun 3.
The quality of model structures generated by contemporary protein structure prediction methods strongly depends on the degree of similarity between the target and available template structures. Therefore, the importance of improving template-based model structures beyond the accuracy available from template information has been emphasized in the structure prediction community. The GalaxyRefine web server, freely available at http://galaxy.seoklab.org/refine, is based on a refinement method that has been successfully tested in CASP10. The method first rebuilds side chains and performs side-chain repacking and subsequent overall structure relaxation by molecular dynamics simulation. According to the CASP10 assessment, this method showed the best performance in improving the local structure quality. The method can improve both global and local structure quality on average, when used for refining the models generated by state-of-the-art protein structure prediction servers.
当代蛋白质结构预测方法生成的模型结构的质量在很大程度上取决于目标结构与可用模板结构之间的相似程度。因此，在结构预测领域，强调了改进基于模板的模型结构，使其超越模板信息提供的准确性。GalaxyRefine 网络服务器可免费使用，网址为 http://galaxy.seoklab.org/refine，它基于一种已在 CASP10 中成功测试的精修方法。该方法首先重建侧链，并通过分子动力学模拟进行侧链重新组装和随后的整体结构松弛。根据 CASP10 的评估，该方法在改善局部结构质量方面表现最佳。当用于精修最先进的蛋白质结构预测服务器生成的模型时，该方法平均可以提高全局和局部结构质量。
