Chivian Dylan, Kim David E, Malmström Lars, Bradley Philip, Robertson Timothy, Murphy Paul, Strauss Charles E M, Bonneau Richard, Rohl Carol A, Baker David
University of Washington, Seattle 98195, USA.
Proteins. 2003;53 Suppl 6:524-33. doi: 10.1002/prot.10529.
Robetta is a fully automated protein structure prediction server that uses the Rosetta fragment-insertion method. It combines template-based and de novo structure prediction methods in an attempt to produce high quality models that cover every residue of a submitted sequence. The first step in the procedure is the automatic detection of the locations of domains and selection of the appropriate modeling protocol for each domain. For domains matched to a homolog with an experimentally characterized structure by PSI-BLAST or Pcons2, Robetta uses a new alignment method, called K*Sync, to align the query sequence onto the parent structure. It then models the variable regions by allowing them to explore conformational space with fragments in fashion similar to the de novo protocol, but in the context of the template. When no structural homolog is available, domains are modeled with the Rosetta de novo protocol, which allows the full length of the domain to explore conformational space via fragment-insertion, producing a large decoy ensemble from which the final models are selected. The Robetta server produced quite reasonable predictions for targets in the recent CASP-5 and CAFASP-3 experiments, some of which were at the level of the best human predictions.
Robetta是一个完全自动化的蛋白质结构预测服务器，它使用Rosetta片段插入方法。它结合了基于模板和从头开始的结构预测方法，试图生成高质量的模型，覆盖提交序列的每个残基。该过程的第一步是自动检测结构域的位置，并为每个结构域选择合适的建模协议。对于通过PSI-BLAST或Pcons2与具有实验表征结构的同源物匹配的结构域，Robetta使用一种称为K*Sync的新比对方法，将查询序列比对到母体结构上。然后，它通过允许可变区域以类似于从头开始协议的方式用片段探索构象空间来对可变区域进行建模，但这是在模板的背景下进行的。当没有可用的结构同源物时，使用Rosetta从头开始协议对结构域进行建模，该协议允许结构域的全长通过片段插入来探索构象空间，生成大量的诱饵集合，最终模型将从中选择。在最近的CASP-5和CAFASP-3实验中，Robetta服务器对目标产生了相当合理的预测，其中一些预测达到了最佳人类预测的水平。
