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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:

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 , 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.

Conserved domains and protein classification

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 of multiple sequence alignments representing conserved domains, in addition to that use 3D-structure information explicitly to define domain boundaries and provide insights into relationships.

Small molecules and their biological activity

The PubChem project provides information on the biological activities of small molecules. PubChem includes three databases: Substance, BioAssay, and Compound. Links among the databases make it possible, for example, to traverse from a compound to its biological activity data, and to retrieve 3D protein structures bound to the compound, interactively view their active sites, and find biosystems that include the compound as a component.

Biological Systems

A , 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 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 , , and involved in a biological system. The companion

FLink tool, in turn, allows you to a list of proteins, genes, or small molecules and retrieve a of biosystems.

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