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FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties.

Abstract：

:FUGUE, a program for recognizing distant homologues by sequence-structure comparison (http://www-cryst.bioc.cam.ac.uk/fugue/), has three key features. (1) Improved environment-specific substitution tables. Substitutions of an amino acid in a protein structure are constrained by its local structural environment, which can be defined in terms of secondary structure, solvent accessibility, and hydrogen bonding status. The environment-specific substitution tables have been derived from structural alignments in the HOMSTRAD database (http://www-cryst.bioc. cam.ac.uk/homstrad/). (2) Automatic selection of alignment algorithm with detailed structure-dependent gap penalties. FUGUE uses the global-local algorithm to align a sequence-structure pair when they greatly differ in length and uses the global algorithm in other cases. The gap penalty at each position of the structure is determined according to its solvent accessibility, its position relative to the secondary structure elements (SSEs) and the conservation of the SSEs. (3) Combined information from both multiple sequences and multiple structures. FUGUE is designed to align multiple sequences against multiple structures to enrich the conservation/variation information. We demonstrate that the combination of these three key features implemented in FUGUE improves both homology recognition performance and alignment accuracy.

journal_name

J Mol Biol

journal_title

Journal of molecular biology

authors

Shi J,Blundell TL,Mizuguchi K

doi

10.1006/jmbi.2001.4762

keywords:

subject

Has Abstract

pub_date

2001-06-29 00:00:00

pages

243-57

issue

1

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(01)94762-X

journal_volume

310

pub_type

杂志文章

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