Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
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DOI：
10.1006/jmbi.1997.0959
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发表时间：
1997-04-25
影响因子：
5.6
通讯作者：
Baker, D
中科院分区：
文献类型：
--
作者：
Simons, KT;Kooperberg, C;Baker, D
我们探讨了一个简单的模拟退火过程组装本地类似的结构，从片段的不相关的蛋白质结构相似的局部序列使用贝叶斯评分函数的能力。环境和残基对具体贡献的评分函数出现在一系列扩展的蛋白质数据库中的残基概率分布的前两项;解耦的距离和环境的依赖性的分布解决了主要问题，与当前的数据库衍生的评分函数注意到托马斯和迪尔。模拟退火过程快速且频繁地产生小螺旋蛋白质的天然样结构，并且比含有蛋白质的小β折叠的随机结构更好。大多数模拟的结构具有天然的溶剂可及性和二级结构模式，因此这些结构的集合提供了一组特别具有挑战性的诱饵，用于评估评分功能。我们研究了多序列信息和不同类型的构象约束对该方法的整体性能的影响，以及各种最近开发的评分函数识别模拟结构的集合中的天然构象的能力。(C)出版社：Academic Press Limited。
We explore the ability of a simple simulated annealing procedure to assemble native-like structures from fragments of unrelated protein structures with similar local sequences using Bayesian scoring functions. Environment and residue pair specific contributions to the scoring functions appear as the first two terms in a series expansion for the residue probability distributions in the protein database; the decoupling of the distance and environment dependencies of the distributions resolves the major problems with current database-derived scoring functions noted by Thomas and Dill. The simulated annealing procedure rapidly and frequently generates native-like structures for small helical proteins and better than random structures for small beta sheet containing proteins. Most of the simulated structures have native-like solvent accessibility and secondary structure patterns, and thus ensembles of these structures provide a particularly challenging set of decoys for evaluating scoring functions. We investigate the effects of multiple sequence information and different types of conformational constraints on the overall performance of the method, and the ability of a variety of recently developed scoring functions to recognize the native-like conformations in the ensembles of simulated structures. (C) 1997 Academic Press Limited.