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Recognition of related proteins by iterative template refinement (ITR)
Author(s) -
Yi TauMu,
Lander Eric S.
Publication year - 1994
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1002/pro.5560030818
Subject(s) - template , computer science , sequence (biology) , protein structure database , computational biology , protein structure , protein structure prediction , set (abstract data type) , loop modeling , similarity (geometry) , structural similarity , structural classification of proteins database , iterative and incremental development , artificial intelligence , biology , sequence database , genetics , biochemistry , programming language , image (mathematics) , software engineering , gene
Predicting the structural fold of a protein is an important and challenging problem. Available computer programs for determining whether a protein sequence is compatible with a known 3‐dimensional structure fall into 2 categories: (1) structure‐based methods, in which structural features such as local conformation and solvent accessibility are encoded in a template, and (2) sequence‐based methods, in which aligned sequences of a set of related proteins are encoded in a template. In both cases, the programs use a static template based on a predetermined set of proteins. Here, we describe a computer‐based method, called iterative template refinement (ITR), that uses templates combining structure‐based and sequence‐based information and employs an iterative search procedure to detect related proteins and sequentially add them to the templates. Starting from a single protein of known structure, ITR performs sequential cycles of database search to construct an expanding tree of templates with the aim of identifying subtle relationships among proteins. Evaluating the performance of ITR on 6 proteins, we found that the method automatically identified a variety of subtle structural similarities to other proteins. For example, the method identified structural similarity between arabinose‐binding protein and phosphofructokinase, a relationship that has not been widely recognized.