NDLI: Recognition of related proteins by iterative template refinement (ITR).

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Recognition of related proteins by iterative template refinement (ITR).

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Recognition of related proteins by iterative template refinement (ITR).

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Lander, E. S. Yi, T. M.
Description	Author Affiliation: Yi TM ( Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge 02142.)
Abstract	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.
ISSN	09618368
e-ISSN	1469896X
Journal	Protein Science
Issue Number	8
Volume Number	3
Language	English
Publisher	Wiley-Blackwell (on behalf of The Protein Society)
Publisher Date	1994-08-01
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Information Storage And Retrieval Proteins Chemistry Sequence Homology Templates, Genetic Amino Acid Sequence Binding Sites Carrier Proteins Chymotrypsin Cytochrome c Group Databases, Factual Escherichia Coli Proteins L-lactate Dehydrogenase Molecular Sequence Data Plastocyanin Tryptophan Synthase Comparative Study Research Support, Non-u.s. Gov't Research Support, U.s. Gov't, Non-p.h.s. Research Support, U.s. Gov't, P.h.s. Discipline Biochemistry
Content Type	Text
Resource Type	Article
Subject	Medicine Molecular Biology Biochemistry

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