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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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BioSystems, a database of biological systems, containing records of molecules that
interact within each system. One type of biosystem is a biological pathway, which can consist of interacting genes, proteins, and small molecules.
Another type of biosystem is a disease, which can involve components such as genes, biomarkers, and drugs.
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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 PubMed documents;
- get taxonomy information;
- view sequence neighbors;
- view structure neighbors.
- access information about small molecules.
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The NCBI BioSystems Database was developed as a collaborative and
complementary project to existing pathways databases to collect annotated
"groups of molecules", which interact in biological systems such as pathways
or functional complexes. BioSystems may contain genes, proteins, and small
molecules, and define functional links between them. NCBI BioSystems: (1)
serves as a centralized data repository; (2) connects the biosystem records
with associated literature, molecular, and chemical data throughout the
Entrez system; and (3) facilitates computation on biosystems data.