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PMID: 8035212 Published · ppublish English Comparative Study Journal Article

Structure-based identification and clustering of protein families and superfamilies.

Journal of computer-aided molecular design ·Vol. 8 ·No. 1 ·1994-02-00 ·Pages 5-27

Rufino SD, Blundell TL

Abstract

We describe an approach to protein structure comparison designed to detect distantly related proteins of similar fold, where the procedure must be sufficiently flexible to take into account the elasticity of protein folds without losing specificity. Protein structures are represented as a series of secondary structure elements, where for each element a local environment describes its relations with the elements that surround it. Secondary structures are then aligned by comparing their features and local environments. The procedure is illustrated with searches of a database of 468 protein structures in order to identify proteins of similar topology to porcine pepsin, porphobilinogen deaminase and serum amyloid P-component. In all cases the searches correctly identify protein structures of similar fold as the search proteins. Multiple cross-comparisons of protein structures allow the clustering of proteins of similar fold. This is exemplified with a clustering of alpha/beta- and beta-class protein structures. We discuss applications of the comparison and clustering of three-dimensional protein structures to comparative modelling and structure-based protein design.

MeSH Terms
Algorithms Amino Acid Sequence Animals Databases, Factual Drug Design Endopeptidases/chemistry Hydrogen Bonding Hydroxymethylbilane Synthase/chemistry Models, Molecular Molecular Sequence Data Pepsin A/chemistry Protein Conformation Protein Folding Protein Structure, Secondary Proteins/chemistry,classification Retroviridae Proteins/chemistry Serum Amyloid P-Component/chemistry Software Swine
Chemicals
Proteins Retroviridae Proteins Serum Amyloid P-Component Hydroxymethylbilane Synthase Endopeptidases Pepsin A
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Rufino S D
Department of Crystallography, Birkbeck College, University of London, U.K.
Blundell T L
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Article Info
Journal
Journal of computer-aided molecular design
Abbr.
J Comput Aided Mol Des
ISSN
0920-654X
DOI
10.1007/BF00124346
Published
1994-02-00
Pages
5-27
Language
English
Region
Netherlands
NLM ID
8710425
Subset
IM
External Links
PubMed source DOI: 10.1007/BF00124346 View journal details
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