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3D Macromolecular Structures

Conserved Domains

The NCBI Structure Group

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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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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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 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:

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.

| Revised 30 January 2012 |

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