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首页> 外文期刊>Journal of Molecular Biology >GLOBAL OPTIMUM PROTEIN THREADING WITH GAPPED ALIGNMENT AND EMPIRICAL PAIR SCORE FUNCTIONS
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GLOBAL OPTIMUM PROTEIN THREADING WITH GAPPED ALIGNMENT AND EMPIRICAL PAIR SCORE FUNCTIONS

机译：具有间隙对齐和经验对得分函数的全局最佳蛋白质线程

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We describe a branch-and-bound search algorithm for finding the exact global optimum gapped sequence-structure alignment (''threading'') between a protein sequence and a protein core or structural model, using an arbitrary amino acid pair score function (e.g. contact potentials, knowledge-based potentials, potentials of mean force, etc.). The search method imposes minimal conditions on how structural environments are defined or the form of the score function, and allows arbitrary sequence-specific functions for scoring loops and active site residues. Consequently the search method can be used with many different score functions and threading methodologies; this paper illustrates five from the literature. On a desktop workstation running LISP, we have found the global optimum protein sequence-structure alignment in NP-hard search spaces as large as 9.6 x 10(31), at rates ranging as high as 6.8 x 10(28) equivalent threadings per second (most of which are pruned before they ever are examined explicitly). Continuing the procedure past the global optimum enumerates successive candidate threadings in monotonically increasing score order. We give efficient algorithms for search space size, uniform random sampling, segment placement probabilities, mean, standard deviation and partition function. The method should prove useful for structure prediction, as well as for critical evaluation of new pair score functions. (C) 1996 Academic Press Limited [References: 70]
机译：我们描述了一种分支定界搜索算法，该算法使用任意氨基酸对得分函数（例如，）在蛋白质序列与蛋白质核心或结构模型之间寻找确切的全局最佳缺口序列结构比对（“线程化”）接触电势，基于知识的电势，平均力电势等）。该搜索方法对如何定义结构环境或得分函数的形式施加了最低限度的条件，并允许对得分环和活性位点残基进行评分的任意特定于序列的函数。因此，搜索方法可以与许多不同的得分函数和线程方法一起使用。本文从文献中举例说明了五种。在运行LISP的台式工作站上，我们发现NP硬搜索空间中的全局最佳蛋白质序列结构比对高达9.6 x 10（31），速率高达每秒6.8 x 10（28）个等效线程（其中大多数都在被明确检查之前被修剪）。继续执行过程，使其超过全局最优值，将以单调递增的分数顺序枚举连续的候选线程。我们为搜索空间大小，统一随机抽样，段放置概率，均值，标准差和分区函数提供了有效的算法。该方法应被证明对结构预测以及对新的配对得分函数的严格评估有用。 （C）1996 Academic Press Limited [参考号：70]

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