MMDB and VAST+: tracking structural similarities between macromolecular complexes.

ABSTRACT: 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 presen

SUBMITTER: Madej T 

PROVIDER: S-EPMC3965051 | biostudies-literature | 2014 Jan

REPOSITORIES: biostudies-literature