Nucleic Acids Research, Vol 27, Issue 1 240-243, Copyright © 1999 by Oxford University Press
A Marchler-Bauer, KJ Addess, C Chappey, L Geer, T Madej, Y Matsuo, Y Wang and SH Bryant
The three dimensional structures for representatives of nearly half of all
protein families are now available in public databases. Thus, no matter
which protein one investigates, it is increasingly likely that the 3D
structure of a homolog will be known and may reveal unsuspected
structure-function relationships. The goal of Entrez's 3D-structure
database is to make this information accessible and usable by molecular
biologists (http://www.ncbi.nlm.nih.gov/Entrez). To this end Entrez
provides two major analysis tools, a search engine based on sequence and
structure 'neighboring' and an integrated visualization system for sequence
and structure alignments. From a protein's sequence 'neighbors' one may
rapidly identify other members of a protein family, including those where
3D structure is known. By comparing aligned sequences and/or structures in
detail, using the visualization system, one may identify conserved features
and perhaps infer functional properties. Here we describe how these
analysis tools may be used to investigate the structure and function of
newly discovered proteins, using the PTEN gene product as an example.
ARTICLES
MMDB: Entrez's 3D structure database
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
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