TY - JOUR

T1 - SITEX 2.0

T2 - Projections of protein functional sites on eukaryotic genes. Extension with orthologous genes

AU - Medvedeva, Irina V.

AU - Demenkov, Pavel S.

AU - Ivanisenko, Vladimir A.

PY - 2017/4/1

Y1 - 2017/4/1

N2 - Functional sites define the diversity of protein functions and are the central object of research of the structural and functional organization of proteins. The mechanisms underlying protein functional sites emergence and their variability during evolution are distinguished by duplication, shuffling, insertion and deletion of the exons in genes. The study of the correlation between a site structure and exon structure serves as the basis for the in-depth understanding of sites organization. In this regard, the development of programming resources that allow the realization of the mutual projection of exon structure of genes and primary and tertiary structures of encoded proteins is still the actual problem. Previously, we developed the SitEx system that provides information about protein and gene sequences with mapped exon borders and protein functional sites amino acid positions. The database included information on proteins with known 3D structure. However, data with respect to orthologs was not available. Therefore, we added the projection of sites positions to the exon structures of orthologs in SitEx 2.0. We implemented a search through database using site conservation variability and site discontinuity through exon structure. Inclusion of the information on orthologs allowed to expand the possibilities of SitEx usage for solving problems regarding the analysis of the structural and functional organization of proteins. Database URL: http://www-bionet.sscc.ru/sitex/.

AB - Functional sites define the diversity of protein functions and are the central object of research of the structural and functional organization of proteins. The mechanisms underlying protein functional sites emergence and their variability during evolution are distinguished by duplication, shuffling, insertion and deletion of the exons in genes. The study of the correlation between a site structure and exon structure serves as the basis for the in-depth understanding of sites organization. In this regard, the development of programming resources that allow the realization of the mutual projection of exon structure of genes and primary and tertiary structures of encoded proteins is still the actual problem. Previously, we developed the SitEx system that provides information about protein and gene sequences with mapped exon borders and protein functional sites amino acid positions. The database included information on proteins with known 3D structure. However, data with respect to orthologs was not available. Therefore, we added the projection of sites positions to the exon structures of orthologs in SitEx 2.0. We implemented a search through database using site conservation variability and site discontinuity through exon structure. Inclusion of the information on orthologs allowed to expand the possibilities of SitEx usage for solving problems regarding the analysis of the structural and functional organization of proteins. Database URL: http://www-bionet.sscc.ru/sitex/.

KW - apoptosis

KW - Exon structure

KW - protein functional sites

KW - Animals

KW - Exons

KW - Humans

KW - Software

KW - Computational Biology/methods

KW - Eukaryota/genetics

KW - Apoptosis/genetics

KW - Proteins/genetics

KW - Databases, Factual

KW - ANIMALS

KW - SEQUENCES

KW - DEATH

KW - EVOLUTION

KW - DATABASE

KW - FAMILIES

KW - ARCHITECTURE

UR - http://www.scopus.com/inward/record.url?scp=85010874944&partnerID=8YFLogxK

U2 - 10.1142/S021972001650044X

DO - 10.1142/S021972001650044X

M3 - Article

C2 - 28110602

AN - SCOPUS:85010874944

VL - 15

SP - 1650044

JO - Journal of Bioinformatics and Computational Biology

JF - Journal of Bioinformatics and Computational Biology

SN - 0219-7200

IS - 2

M1 - 1650044

ER -