Department of Biomedical Engineering, Boston University, Boston, Massachusetts.
Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York.
Proteins. 2019 Dec;87(12):1241-1248. doi: 10.1002/prot.25808. Epub 2019 Oct 1.
As a participant in the joint CASP13-CAPRI46 assessment, the ClusPro server debuted its new template-based modeling functionality. The addition of this feature, called ClusPro TBM, was motivated by the previous CASP-CAPRI assessments and by the proven ability of template-based methods to produce higher-quality models, provided templates are available. In prior assessments, ClusPro submissions consisted of models that were produced via free docking of pre-generated homology models. This method was successful in terms of the number of acceptable predictions across targets; however, analysis of results showed that purely template-based methods produced a substantially higher number of medium-quality models for targets for which there were good templates available. The addition of template-based modeling has expanded ClusPro's ability to produce higher accuracy predictions, primarily for homomeric but also for some heteromeric targets. Here we review the newest additions to the ClusPro web server and discuss examples of CASP-CAPRI targets that continue to drive further development. We also describe ongoing work not yet implemented in the server. This includes the development of methods to improve template-based models and the use of co-evolutionary information for data-assisted free docking.
作为 CASP13-CAPRI46 评估的参与者之一，ClusPro 服务器推出了其新的基于模板的建模功能。添加此功能（称为 ClusPro TBM）的动机是之前的 CASP-CAPRI 评估以及基于模板的方法在有可用模板的情况下能够产生更高质量模型的能力。在之前的评估中，ClusPro 的提交内容由通过预生成的同源模型自由对接生成的模型组成。就跨目标的可接受预测数量而言，这种方法是成功的；然而，结果分析表明，对于有良好模板可用的目标，纯粹基于模板的方法产生了大量数量的中等质量模型。基于模板的建模的添加扩展了 ClusPro 生成更高准确性预测的能力，主要针对同型但也针对一些异型目标。在这里，我们回顾了 ClusPro 网络服务器的最新添加内容，并讨论了继续推动进一步发展的 CASP-CAPRI 目标的示例。我们还描述了尚未在服务器中实现的正在进行的工作。这包括开发用于改进基于模板的模型的方法以及使用共进化信息进行数据辅助的自由对接。
