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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, computationally identified 3D domains (compact substructures) that are used to identify similar 3D structures, as well as links to literature, similar sequences, 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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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. 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 an alignment of the query protein to the related structure's sequence and allows you to interactively examine the sequence-structure relationship.
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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 similar structures, and conserved core motifs identified in conserved domains.
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IBIS |
IBIS is the NCBI Inferred Biomolecular Interaction Server, which organizes, analyzes and predicts interaction partners and locations of binding sites in
proteins. IBIS provides annotations for different types of binding partners: protein, chemical, nucleic acid, peptides and ions. IBIS reports interactions observed in experimentally determined structural complexes of a given protein, and at the same time infers binding sites/interacting partners by inspecting protein complexes formed by homologous proteins. Similar binding sites are clustered together based on their sequence and structure conservation. To emphasize biologically
relevant binding sites, several algorithms are used for verification in terms of evolutionary conservation, biological importance of binding partners, size and stability of interfaces, as well as evidence
from the published literature.
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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. "Similar 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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