About: MMDB: annotating protein sequences with Entrez's 3D-structure database

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An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	MMDB: annotating protein sequences with Entrez's 3D-structure database
Creator	Wang, Yanli Chen, Jie He, Jane He, Siqian Lu, Shennan Madej, Thomas Marchler-Bauer, Aron Zhang, Naigong Bryant, Stephen Addess, Kenneth Geer, Lewis Thiessen, Paul
source	Medline; PMC
abstract	Three-dimensional (3D) structure is now known for a large fraction of all protein families. Thus, it has become rather likely that one will find a homolog with known 3D structure when searching a sequence database with an arbitrary query sequence. Depending on the extent of similarity, such neighbor relationships may allow one to infer biological function and to identify functional sites such as binding motifs or catalytic centers. Entrez's 3D-structure database, the Molecular Modeling Database (MMDB), provides easy access to the richness of 3D structure data and its large potential for functional annotation. Entrez's search engine offers several tools to assist biologist users: (i) links between databases, such as between protein sequences and structures, (ii) pre-computed sequence and structure neighbors, (iii) visualization of structure and sequence/structure alignment. Here, we describe an annotation service that combines some of these tools automatically, Entrez's ‘Related Structure’ links. For all proteins in Entrez, similar sequences with known 3D structure are detected by BLAST and alignments are recorded. The ‘Related Structure’ service summarizes this information and presents 3D views mapping sequence residues onto all 3D structures available in MMDB ().
has issue date	2006-11-29(xsd:dateTime)
bibo:doi	10.1093/nar/gkl952
bibo:pmid	17135201
has license	cc-by-nc
sha1sum (hex)	c62da850c36f3f10a1fa9289548460fa51b95f26
schema:url	https://doi.org/10.1093/nar/gkl952
resource representing a document's title	MMDB: annotating protein sequences with Entrez's 3D-structure database
has PubMed Central identifier	PMC1751549
has PubMed identifier	17135201
schema:publication	Nucleic Acids Res
resource representing a document's body	covid:c62da850c36f3f10a1fa9289548460fa51b95f26#body_text
is schema:about of	named entity '3D-STRUCTURE' named entity 'RICHNESS' named entity 'PROTEINS' named entity 'THESE' named entity 'BINDING' named entity 'SIMILARITY' named entity 'PRESENTS' named entity 'SEQUENCES' named entity 'HERE' named entity 'CATALYTIC' named entity 'STRUCTURES' named entity 'EASY' named entity 'LIKELY' named entity 'STRUCTURE' named entity 'LARGE' named entity 'LINKS' named entity 'NLM' named entity 'DATABASES' named entity 'INFORMATION' named entity '3D-STRUCTURE' named entity 'COMBINES' named entity 'VISUALIZATION' named entity 'NIH' named entity 'INFER' named entity 'GOV' named entity 'TO IDENTIFY' named entity 'VIEWS' named entity '27S' named entity 'SEQUENCE' named entity 'SEQUENCE DATABASE' named entity 'MMDB' named entity 'RECORDED' named entity 'TOOLS' named entity 'database' named entity 'structure' named entity 'arbitrary' named entity 'binding' named entity 'sequence' named entity 'describe' named entity 'Entrez' named entity 'RATHER' named entity 'ALLOW' named entity 'DETECTED' named entity 'MMDB' named entity 'FUNCTIONAL SITES' named entity 'ANNOTATION' named entity 'ENTREZ' named entity 'FRACTION OF' named entity 'CENTERS' named entity 'PROTEIN SEQUENCES' named entity 'AVAILABLE' named entity 'ARBITRARY' named entity 'ENTREZ' named entity 'DATABASE' named entity '27S' named entity 'PROTEIN SEQUENCES' named entity 'THREE-DIMENSIONAL' named entity 'RELATIONSHIPS' named entity 'QUERY' named entity 'DATABASE' named entity 'BIOLOGICAL FUNCTION' named entity 'USERS' named entity 'SEARCH ENGINE' named entity 'BIOLOGIST' named entity 'AUTOMATICALLY' named entity 'ALIGNMENT' named entity 'KNOWN' named entity 'HOMOLOG' named entity 'MAPPING' named entity 'NEIGHBOR'

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