Xie Wei, Sahinidis Nikolaos V
Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign 600 South Mathews Avenue, Urbana, IL 61801, USA.
Bioinformatics. 2006 Jan 15;22(2):188-94. doi: 10.1093/bioinformatics/bti763. Epub 2005 Nov 8.
The protein side-chain conformation problem is a central problem in proteomics with wide applications in protein structure prediction and design. Computational complexity results show that the problem is hard to solve. Yet, instances from realistic applications are large and demand fast and reliable algorithms.
We propose a new global optimization algorithm, which for the first time integrates residue reduction and rotamer reduction techniques previously developed for the protein side-chain conformation problem. We show that the proposed approach simplifies dramatically the topology of the underlining residue graph. Computations show that our algorithm solves problems using only 1-10% of the time required by the mixed-integer linear programming approach available in the literature. In addition, on a set of hard side-chain conformation problems, our algorithm runs 2-78 times faster than SCWRL 3.0, which is widely used for solving these problems.
The implementation is available as an online server at http://eudoxus.scs.uiuc.edu/r3.html
蛋白质侧链构象问题是蛋白质组学中的核心问题，在蛋白质结构预测和设计中有广泛应用。计算复杂性结果表明该问题难以解决。然而，实际应用中的实例规模较大，需要快速且可靠的算法。
我们提出了一种新的全局优化算法，该算法首次整合了先前为蛋白质侧链构象问题开发的残基约简和旋转异构体约简技术。我们表明，所提出的方法极大地简化了基础残基图的拓扑结构。计算表明，我们的算法解决问题所需的时间仅为文献中可用的混合整数线性规划方法所需时间的1% - 10%。此外，在一组困难的侧链构象问题上，我们的算法比广泛用于解决这些问题的SCWRL 3.0快2 - 78倍。
该实现可作为在线服务器在http://eudoxus.scs.uiuc.edu/r3.html获取。
