SitEx: a computer system for analysis of projections of protein functional sites on eukaryotic genes.

Abstract:

:Search of interrelationships between the structural-functional protein organization and exon structure of encoding gene provides insights into issues concerned with the function, origin and evolution of genes and proteins. The functions of proteins and their domains are defined mostly by functional sites. The relation of the exon-intron structure of the gene to the protein functional sites has been little studied. Development of resources containing data on projections of protein functional sites on eukaryotic genes is needed. We have developed SitEx, a database that contains information on functional site amino acid positions in the exon structure of encoding gene. SitEx is integrated with the BLAST and 3DExonScan programs. BLAST is used for searching sequence similarity between the query protein and polypeptides encoded by single exons stored in SitEx. The 3DExonScan program is used for searching for structural similarity of the given protein with these polypeptides using superimpositions. The developed computer system allows users to analyze the coding features of functional sites by taking into account the exon structure of the gene, to detect the exons involved in shuffling in protein evolution, also to design protein-engineering experiments. SitEx is accessible at http://www-bionet.sscc.ru/sitex/. Currently, it contains information about 9994 functional sites presented in 2021 proteins described in proteomes of 17 organisms.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Medvedeva I,Demenkov P,Kolchanov N,Ivanisenko V

doi

10.1093/nar/gkr1187

subject

Has Abstract

pub_date

2012-01-01 00:00:00

pages

D278-83

issue

Database issue

eissn

0305-1048

issn

1362-4962

pii

gkr1187

journal_volume

40

pub_type

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