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Molecular Modeling Database (MMDB) |
Experimentally resolved structures of proteins, RNA, and DNA, derived from the Protein Data Bank (PDB), with value-added features such as explicit chemical graphs, links to literature, similar sequences, related 3D structures, information about chemicals bound to the structures, and more. These connections make it possible, for example, to find 3D structures for homologs of a protein sequence of interest, then interactively view the sequence-structure relationships, active sites, bound chemicals, journal articles, and more.
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3D Domains |
The 3D Domains database is derived from and extensively linked with MMDB. 3D domains are compact structural units within a protein that are identified automatically in MMDB using purely geometric criteria. A protein chain can contain one or more 3D domains, which often correspond with conserved domains (illustrated example) observed in molecular evolution. Additionally, proteins that are dissimilar in sequence might contain geometrically similar 3D domains, indicating a distant homology that cannot be recognized by sequence comparison. 3D domains are used in the identification of VAST related structures, described below.
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CBLAST |
A tool that compares a query protein sequence against all protein sequences from resolved 3D structures by using protein BLAST against the PDB data set. The purpose is to find representative 3D structures for the query and/or its homologs, as available. Each record in the Entrez Protein database has been CBLAST'ed and the search results are available as Related Structures in the "Links" menu of Entrez Protein records (illustrated example). You can also enter a protein query sequence directly into the CBLAST search page in order to find its sequence-similar 3D structure records. The search results can be viewed in Cn3D (hence the name "CBLAST"), which displays a sequence alignment of the query and the hit as well as the corresponding 3D structure.
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Cn3D |
A tool for visualization of three-dimensional structures with emphasis on interactive examination of sequence-structure relationships and superposition of geometrically similar structures. Can be used to display MMDB structures, superpositions of VAST related structures, and conserved core motifs identified in conserved domains.
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Vector Alignment Search Tool (VAST) |
A computer algorithm developed at NCBI and used to identify similar protein 3-dimensional structures by purely geometric criteria, and to identify distant homologs that cannot be recognized by sequence comparison. "Related structures" for every structure in MMDB are pre-computed using VAST and accessible via links on the MMDB Structure Summary pages. The VAST Search page also allows you to compare the coordinates of a newly resolved structure in PDB format against all structures in MMDB to find its neighbors.
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