The NCBI Structure Group maintains:
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MMDB, a database of macromolecular 3D structures, as well as tools for their visualization and comparative analysis. MMDB, the
Molecular Modelling DataBase, contains experimentally determined biopolymer structures obtained from the
Protein Data Bank (PDB).
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PubVast, a database of structure-structure alignments. Each protein chain and 3D domain from
MMDB is compared with all the others using the VAST (Vector Alignment Search Tool) algorithm.
Lists of VAST neighbors are available via links on the MMDB Structure Summary pages, and structural
superpositions may be displayed with the visualization tool Cn3D.
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PubChem, a database of small molecules, which provides information on their biological
activities. It is a component of NIH's Molecular Libraries Roadmap Initiative..
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CDD, the Conserved Domain Database, a protein
annotation resource, which consists of a collection of well-annotated multiple sequence alignment models for ancient domains and
full-length proteins. These are available as position-specific score matrices (PSSMs), for the rapid identification of conserved domains
in protein sequences.
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Text searches in Entrez/MMDB will yield
Structure Query pages, providing access to entries which matched the keywords.
Structure Summary pages for one/several/all of these may be retrieved.
From the Structure Summary pages one may:
- access amino acid and nucleic acid sequences;
- retrieve MedLine documents;
- get taxonomy information;
- view sequence neighbors;
- view structure neighbors.
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MMDB now contains about 48,000 entries. They can be anything from short
oligonucleotides or peptides to very large macromolecular complexes
containing dozens of individual molecules. A more extensive description
and help on using MMDB are available..