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Graph‐based methods for protein structure comparison
Author(s) -
Fober Thomas,
Mernberger Marco,
Klebe Gerhard,
Hüllermeier Eyke
Publication year - 2013
Publication title -
wiley interdisciplinary reviews: data mining and knowledge discovery
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.506
H-Index - 47
eISSN - 1942-4795
pISSN - 1942-4787
DOI - 10.1002/widm.1099
Subject(s) - computer science , inference , rotation formalisms in three dimensions , graph , protein structure database , protein function prediction , theoretical computer science , sequence (biology) , protein structure prediction , similarity (geometry) , data mining , protein structure , algorithm , artificial intelligence , protein function , sequence database , mathematics , biology , biochemistry , genetics , geometry , gene , image (mathematics)
While sequence‐based methods are widely used as reliable tools for protein function prediction in general, these methods are likely to fail in cases of low sequence similarity. This is due to the fact that proteins with low sequence similarity may nevertheless have similar functions and exhibit similar structures. In such cases, structure‐based comparison methods can help to provide further insights owing to the widely accepted paradigm that structure mirrors function. Moreover, thanks to the steady increase in structural information with the advent of structural genomic projects and the steady improvements in structure prediction, these methods are becoming more and more applicable. Many structure‐based approaches to the comparative analysis of proteins and the inference of protein function rely on graph formalisms for modeling protein structures and, correspondingly, employ graph‐theoretic algorithms for analyzing and comparing such structures. This review is devoted to approaches of that kind and presents an overview of the most important graph‐based algorithms. This article is categorized under: Algorithmic Development > Biological Data Mining Algorithmic Development > Structure Discovery