Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling
Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling
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DOI：
10.1002/prot.10550
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发表时间：
2003-01-01
期刊：
影响因子：
--
通讯作者：
Honig, B
中科院分区：
文献类型：
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作者：
Petrey, D;Xiang, ZX;Honig, B
我们主要使用内部软件参与CASP 5的折叠识别和同源部分。我们的结构预测策略的核心特征涉及生成良好的序列到结构比对的能力，并将其快速转换为可以使用基于能量的方法和手动评估的模型。我们使用的内部工具包括：a）HMAP（混合多维比对图谱）-一种图谱对图谱比对方法，其源自核心区域中的序列增强的多结构比对和非结构保守区域中的序列基序。B）NEST-应用“人工进化”算法从给定模板和比对构建模型的快速模型构建程序。c）GRASP 2-一种新的结构和比对可视化程序，其结合了多个结构叠加和域数据库扫描模块。这些方法与基于全原子和简化物理化学能量函数的模型评估相结合。所有这些方法都是在CASP 5期间开发的，因此在预测过程的每个阶段都进行了大量的人工分析。这种交互式的模型构建过程有几个优点，并提出了重要的方式，我们和其他方法可以改进，其中提供的例子。(C)2003 Wiley-Liss，Inc.
We participated in the fold recognition and homology sections of CASP5 using primarily in-house software. The central feature of our structure prediction strategy involved the ability to generate good sequence-to-structure alignments and to quickly transform them into models that could be evaluated both with energy-based methods and manually. The in-house tools we used include: a) HMAP (Hybrid Multidimensional Alignment Profile)-a profile-to-profile alignment method that is derived from sequence-enhanced multiple structure alignments in core regions, and sequence motifs in non-structurally conserved regions. b) NEST-a fast model building program that applies an "artificial evolution" algorithm to construct a model from a given template and alignment. c) GRASP2-a new structure and alignment visualization program incorporating multiple structure superposition and domain database scanning modules. These methods were combined with model evaluation based on all atom and simplified physical-chemical energy functions. All of these methods were under development during CASP5 and consequently a great deal of manual analysis was carried out at each stage of the prediction process. This interactive model building procedure has several advantages and suggests important ways in which our and other methods can be improved, examples of which are provided. (C) 2003 Wiley-Liss, Inc.