Databases

3D Domains Database
Contains compact structural domains identified automatically in the macromolecular 3D structure database (MMDB). These domains are identified by searching for breakpoints in the structure between major secondary structure elements so that the ratio of intra- to inter-domain contacts falls above a set threshold. 3D Domains are the units of comparison for structure neighbor (related structures) calculations using the VAST algorithm.
Conserved Domain Database (CDD)
A collection of sequence alignments and profiles representing protein domains conserved in molecular evolution. It also includes alignments of the domains to known 3-dimensional protein structures in the MMDB database.
Structure (Molecular Modeling Database)
Contains macromolecular 3D structures derived from the Protein Data Bank, as well as tools for their visualization and comparative analysis.

Tools

CDTree
A stand-alone application for classifying protein sequences and investigating their evolutionary relationships. CDTree can import, analyze and update existing Conserved Domain (CDD) records and hierarchies, and also allows users to create their own. CDTree is tightly integrated with Entrez CDD and Cn3D, and allows users to create and update protein domain alignments.
Cn3D
A stand-alone application for viewing 3-dimensional structures from NCBI's Entrez retrieval service. Cn3D runs on Windows, Macintosh, and UNIX and can be configured to receive data from most popular web browsers. Cn3D simultaneously displays structure, sequence, and alignment, and has powerful annotation and alignment editing features.
Conserved Domain Architecture Retrieval Tool (CDART)
Displays the functional domains that make up a given protein sequence. It lists proteins with similar domain architectures and can retrieve proteins that contain particular combinations of domains.
Conserved Domain Search Service (CD Search)
Identifies the conserved domains present in a protein sequence. CD-Search uses RPS-BLAST (Reverse Position-Specific BLAST) to compare a query sequence against position-specific score matrices that have been prepared from conserved domain alignments present in the Conserved Domain Database (CDD).
PSSM Viewer
Allows users to display, sort, subset and download position-specific score matrices (PSSMs) either from CDD records or from Position Specific Iterated (PSI)-BLAST protein searches. The tool also can align a query protein to the PSSM and highlight positions of high conservation.
Related Structures
The Related Structures tool allows users to find 3D structures from the Molecular Modeling Database (MMDB) that are similar in sequence to a query protein. Although the query protein may not yet have a resolved structure, the 3D shape of a similar protein sequence can shed light on the putative shape and biological function of the query protein.
Vector Alignment Search Tool (VAST)
A computer algorithm that identifies similar protein 3-dimensional structures. Structure neighbors for every structure in MMDB are pre-computed and accessible via links on the MMDB Structure Summary pages. These neighbors can be used to identify distant homologs that cannot be recognized by sequence comparison alone.

Downloads

CDTree Installation Page
CD Tree is a powerful tool to aid in the classification of protein sequences and investigate their evolutionary relationships; a web-based helper application that allows users to view and manipulate pre-defined protein domain hierarchies; and an integrated software environment organized to help users assimilate large amounts of biological data from various resources
Cn3D Installation Page
A stand-alone application for viewing 3-dimensional structures from NCBI's Entrez retrieval service. Cn3D runs on Windows, Macintosh, and UNIX and can be configured to receive data from most popular web browsers. Cn3D simultaneously displays structure, sequence, and alignment, and has powerful annotation and alignment editing features.
FTP: CDD
This site provides full data records for CDD, along with individual Position Specific Scoring Matrices (PSSMs), mFASTA sequences and annotation data for each conserved domain. See the README file for full details.
FTP: Structure (MMDB)
This site contains ASN.1 data for all records in MMDB along with VAST alignment data and the non-redundant PDB (nr-PDB) data sets. See the README file for more information.