MMDB and VAST+: tracking structural similarities between macromolecular complexes

By T. Madej, Christopher J. Lanczycki, Dachuan Zhang, Paul A. Thiessen, Renata C. Geer, Aron Marchler-Bauer, Stephen H. Bryant. Nucleic Acids Res., 2013

328 citations recorded by the source corpus.

The computational detection of similarities between protein 3D structures has become an indispensable tool for the detection of homologous relationships, the classification of protein families and functional inference. Consequently, numerous algorithms have been developed that facilitate structure comparison, including rapid searches against a steadily growing collection of protein structures. To this end, NCBI’s Molecular Modeling Database (MMDB), which is based on the Protein Data Bank (PDB), maintains a comprehensive and up-to-date archive of protein structure similarities computed with the Vector Alignment Search Tool (VAST). These similarities have been recorded on the level of single proteins and protein domains, comprising in excess of 1.5 billion pairwise alignments. Here we present VAST+, an extension to the existing VAST service, which summarizes and presents structural similarity on the level of biological assemblies or macromolecular complexes. VAST+ simplifies structure neighboring results and shows, for macromolecular complexes tracked in MMDB, lists of similar complexes ranked by the extent of similarity. VAST+ replaces the previous VAST service as the default presentation of structure neighboring data in NCBI’s Entrez query and retrieval system. MMDB and VAST+ can be accessed via http://www.ncbi.nlm.nih.gov/Structure.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/add114ea701ec53a99fc84723cb8bb71ce56efcc

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Citations in the corpus

Expanded microbial genome coverage and improved protein family annotation in the COG database (2014, background): “Each gene entry in a COG is now denoted by its gene index (gi) number in the NCBI protein database and is linked to the respective entry in the NCBI’s RefSeq database (28) which provides links to the nucleotide sequence of the encoding gene in GenBank (29), its chromosomal location in Entrez Gene (3”
PubChem 2019 update: improved access to chemical data (2018, background): “Genomes (KEGG) (21), BioSystems (22), Molecular Modeling Database (MMDB) (23).”
CDD: NCBI's conserved domain database (2014, background): “Table 1 below lists URLs for various entry points into CDD. CDD is part of NCBI’s Entrez search and retrieval system and is cross-linked with other databases, such as Entrez / protein, Entrez / Gene, 3D-structure (MMDB), NCBI BioSystems, PubMed and PubChem.”