The comparison of structures and sequences: alignment, searching and the detection of common folds

Author

Johnson, Mark S. ; Overington, John P. ; Edwards, Yvonne ; May, Alex C W ; Rodionov, Michael A.

Author_Institution

Dept. of Crystallogr., Imperial Cancer Res. Fund Labs., London, UK

Volume

5

fYear

1994

fDate

4-7 Jan. 1994

Firstpage

296

Lastpage

305

Abstract

Describes an approach to the comparison and analysis of protein sequences and three-dimensional (3-D) structures. This includes the alignment of structures (using a combination of a genetic algorithm, dynamic programming and least-squares minimization) the alignment of sequences, the search for related structures/sequences and the detection of common folds. These latter procedures are grounded upon the structural alignment of many protein families and the analysis of amino acid substitutions at matched positions within these alignments. The authors consider the local physico-chemical environment within the structure but also those residue-residue and side-chain to main-chain contacts that may occur at a distance along the sequence.<>

Keywords

biology; dynamic programming; genetic algorithms; least squares approximations; proteins; search problems; alignment; amino acid substitutions; common folds; dynamic programming; genetic algorithm; least-squares minimization; protein sequences; searching; sequences; structural alignment; structures;

fLanguage

English

Publisher

ieee

Conference_Titel

System Sciences, 1994. Proceedings of the Twenty-Seventh Hawaii International Conference on

Conference_Location

Wailea, HI, USA

Print_ISBN

0-8186-5090-7

Type

conf

DOI

10.1109/HICSS.1994.323567

Filename

323567