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The NCBI Structure Group
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Resources for the Scientific Community
The resources developed by the Structure Group of the NCBI Computational Biology Branch (CBB) are freely available to the public and focus on four areas:
Example 3-dimensional structure: Tumor Suppressor P53 Complexed with DNA (accession 1TUP). Click on the image for more information about the structure and for examples of how 3D structures can be used to learn more about proteins and other biomolecules. Macromolecular structures
The three-dimensional structures of biomolecules provide a wealth of information on their biological function and evolutionary relationships. The
Molecular Modeling Database (MMDB), as part of the
Entrez system, facilitates access to structure data by connecting them with associated literature, protein and nucleic acid
sequences,
chemicals,
biomolecular interactions, and more. It is possible, for example, to
find 3D structures for homologs of a protein of interest by following the "
Related Structures" link in an
Entrez Protein sequence record.
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Conserved domain hierarchy showing divergence in a protein family based on phylogenetic relationships of protein sequences and functional properties. Click on the image for a more detailed illustration and additional information about domain family hierarchies. Conserved domains and protein classification
Conserved domains are functional units within a protein that act as building blocks in molecular evolution and recombine in various arrangements to make proteins with different functions. The
Conserved Domain Database (CDD) brings together several
collections of multiple sequence alignments representing conserved domains, in addition to
NCBI-curated domains that use 3D-structure information explicitly to define domain boundaries and provide insights into
sequence/structure/function relationships.
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Resources CDD CD-Search Batch CD-Search CDTree CDART
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The 2-dimensional structure of gleevec, PubChem Compound ID (CID) 5291. Click on the image to open the home page for the PubChem resource group. Small molecules and their biological activity
The PubChem project provides information on the biological activities of small molecules and is a component of NIH's
Molecular Libraries Roadmap Initiative.
PubChem includes three databases:
PCSubstance,
PCBioAssay, and
PCCompound. The PubChem data are
linked to other data types (illustrated example) in the
Entrez system, making it possible, for example, to retrieve information about a compound and then "Link" to its
biological activity data, retrieve
3D protein structures bound to the compound and interactively view their
active sites, and find
biosystems that include the compound as a component.
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PubChem Home PCBioAssay PCCompound PCSubstance
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Example of the data available in the NCBI BioSystems database, which lists and categorizes the components of metabolic pathways, including the genes, proteins, and small molecules, and identifies related biosystems. Click on the image to read more about the BioSystems database. Biological Systems
A
biosystem, or biological system, is a group of molecules that interact directly or indirectly, where the grouping is relevant to the characterization of living matter. The
NCBI BioSystems Database provides centralized access to biological pathways from several
source databases and connects the biosystem records with associated literature, molecular, and chemical data throughout the
Entrez system. BioSystem records
list and categorize components (illustrated example), such as the
genes,
proteins, and
small molecules involved in a biological system. The companion
FLink icon FLink tool, in turn, allows you to
input a list of proteins, genes, or small molecules and retrieve a
ranked list of biosystems.
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Tools for Discovery
Discover associations among previously disparate data Schematic depicting connections among various data types, such as literature, nucleotide and protein sequences, and three-dimensional structures. Click anywhere on this image to open a detailed example of the types of connections that exist and how to access them.
Use Entrez's "Links to Related Data" to follow connections among diseases, genes, protein structures and functions, and more. See an example...
Explore large scale data associations using FLink icon FLink: Use FLink to input lists of gene, protein sequence, or small molecule identifiers and retrieve ranked lists of pathways from the BioSystems database. Click on this image to learn more about FLink.
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