Assessment of RAPTOR's linear programming approach in CAFASP3
Assessment of RAPTOR's linear programming approach in CAFASP3
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DOI：
10.1002/prot.10531
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发表时间：
2003-01-01
影响因子：
2.9
通讯作者：
Li, M
中科院分区：
文献类型：
--
作者：
Xu, JB;Li, M
我们基于线性规划(LP)的数学理论开发了一种新的算法，并在我们的程序Raptor中实现了它。我们的新方法提供了蛋白质穿线问题的优雅公式，在实践中克服了蛋白质穿线的难题，并允许我们使用现有的强大的线性规划软件来获得最优的蛋白质穿线解决方案。CASP5和CAFASP3给了我们第一次公正地测试猛禽的机会。Raptor被CAFASP3组织者评为折叠识别的顶级个人(自动)服务器。在这篇简短的文章中，我们描述了Raptor的LP公式，评估了Raptor在CAFASP3/CASP5中的表现，解释了它为什么会取代其他现有的自动化单独方法，并指出了它的优点、局限性、扩展和改进前景。(C)2003年Wiley-Liss，Inc.
We have developed a new algorithm based on the mathematical theory of linear programming (LP) and implemented it in our program RAPTOR. Our new approach provides an elegant formulation of the protein-threading problem, overcomes the intractability problem of protein threading, in practice, and allows us to use existing powerful linear programming software to obtain optimal protein threading solutions. CASP5 and CAFASP3 gave us the first chance to test RAPTOR in an unbiased way. RAPTOR was ranked as the top individual (automatic) server for fold recognition by the CAFASP3 organizers. In this short article, we describe RAPTOR's LP formulation, assess RAPTOR's performance in CAFASP3/CASP5, explain why it has superceded other existing automatic individual methods, and point out its strengths, limitations, extensions, and prospects for improvement. (C) 2003 Wiley-Liss, Inc.