Parallel Seed-Based Approach to Protein Structure Similarity Detection

被引：1

作者：

Chapuis, Guillaume ^{[1
]}

Le Boudic-Jamin, Mathilde ^{[1
]}

Andonov, Rumen ^{[1
]}

Djidjev, Hristo

Lavenier, Dominique ^{[1
]}

机构：

[1] IRISA Rennes, INRIA, GenScale, Rennes, France

来源：

PARALLEL PROCESSING AND APPLIED MATHEMATICS (PPAM 2013), PT II | 2014年 / 8385卷

关键词：

Protein structure comparison; Parallel computing; Seed-based heuristic; Alignment graph; ALIGNMENT; ALGORITHM;

D O I：

10.1007/978-3-642-55195-6_26

中图分类号：

TP [自动化技术、计算机技术];

学科分类号：

0812 ;

摘要：

Finding similarities between protein structures is a crucial task in molecular biology. Many tools exist for finding an optimal alignment between two proteins. These tools, however, only find one alignment even when multiple similar regions exist. We propose a new parallel heuristic-based approach to structural similarity detection between proteins that discovers multiple pairs of similar regions. We prove that returned alignments have RMSDc and RMSDd lower than a given threshold. Computational complexity is addressed by taking advantage of both fine-and coarse-grain parallelism.

引用

页码：278 / 287

页数：10

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