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首页> 外文期刊>Journal of Molecular Biology >FUGUE: Sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties
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FUGUE: Sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties

机译：FUGUE：使用特定于环境的替代表和依赖结构的空位罚分进行序列-结构同源性识别

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摘要

FUGUE, a program for recognizing distant homologues by sequence-structure comparison (http://www-cryst.bioc.cam.ac.uk/fugue/) has three key features. (1) Improved environment-specific substitution tables. Substitutions of an amino acid in a protein structure are constrained by its local structural environment, which can be defined in terms of secondary structure, solvent accessibility, and hydrogen bonding status. The environment-specific substitution tables have been derived from structural alignments in the HOMSTRAD database (http://www-cryst.bioc.cam.ac.uk/homstrad/). (2) Automatic selection of alignment algorithm with detailed structure-dependent gap penalties. FUGUE uses the global-local algorithm to align a sequence-structure pair when they greatly differ in length and uses the global algorithm in other eases. The gap penalty at each position of the structure is determined according to its solvent accessibility, its position relative to the secondary structure elements (SSEs) and the conservation of the SSEs. (3) Combined information from both multiple sequences and multiple structures. FUGUE is designed to align multiple sequences against multiple structures to enrich the conservation/variation information. We demonstrate that the combination of these three key features implemented in FUGUE improves both homology recognition performance and alignment accuracy. (C) 2001 Academic Press. [References: 64]
机译：FUGUE是一种通过序列结构比较识别远距离同源物的程序（http://www-cryst.bioc.cam.ac.uk/fugue/）具有三个关键功能。 （1）改进了特定于环境的替换表。蛋白质结构中氨基酸的取代受到其局部结构环境的限制，可以通过二级结构，溶剂可及性和氢键状态来定义。特定于环境的替代表是从HOMSTRAD数据库（http://www-cryst.bioc.cam.ac.uk/homstrad/）中的结构比对得出的。 （2）自动选择比对算法，并详细列出与结构有关的空位罚分。当长度长度相差很大时，FUGUE使用全局-局部算法对齐序列结构对，并在其他方面使用全局算法。根据其溶剂可及性，相对于二级结构元素（SSE）的位置以及SSE的保守性，确定结构每个位置的空位罚分。 （3）来自多个序列和多个结构的组合信息。 FUGUE设计用于将多个序列与多个结构进行比对，以丰富保守性/变异性信息。我们证明了在FUGUE中实现的这三个关键特征的组合可以提高同源性识别性能和比对精度。 （C）2001学术出版社。 [参考：64]

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