MMDB: Entrez's 3D structure database.
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.
Marchler-Bauer
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A
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
Addess
K J
KJ
Chappey
C
C
Geer
L
L
Madej
T
T
Matsuo
Y
Y
Wang
Y
Y
Bryant
S H
SH
D000595:Amino Acid Sequence; D017124:Conserved Sequence; D016208:Databases, Factual; D006223:Hamartoma Syndrome, Multiple / Q000235:genetics; D006801:Humans; D016247:Information Storage and Retrieval; D020407:Internet; D008958:Models, Molecular; D009154:Mutation; D051059:PTEN Phosphohydrolase; D010744:Phosphoric Monoester Hydrolases / Q000737:chemistry* / Q000235:genetics; D011487:Protein Conformation; D016415:Sequence Alignment; D013329:Structure-Activity Relationship; D025521:Tumor Suppressor Proteins
D025521:Tumor Suppressor Proteins; D010744:Phosphoric Monoester Hydrolases; D051059:PTEN Phosphohydrolase; C494929:PTEN protein, human