MMDB

MMDB provides access to three-dimensional protein structures and their biological annotations and integrates them with NCBI Entrez, sequence data, classification resources, and PubChem small-molecule structures for structural and functional analysis.

Key Features:

• Integration with Entrez: Links protein 3D structure records with NCBI Entrez entries to connect structural data to corresponding sequences and other biological information.
• Database Links: Provides cross-database links connecting protein sequences to their three-dimensional structures and related annotations.
• Pre-computed Neighbors: Contains pre-computed sequence and structure neighbors to facilitate comparative analysis within protein families.
• Visualization Tools: Includes the Cn3D viewer for visualizing 3D structures and sequence–structure alignments.
• Protein Data Bank mirroring: Mirrors the Protein Data Bank (PDB) contents to represent experimentally determined protein structures.
• Automated comparative analysis: Generates graphical summaries of biological annotations for each 3D structure using automated comparative analyses.
• Pre-computed structural alignments (VAST): Provides pre-computed structural alignments produced by the VAST algorithm to reveal structural neighbors and complexes.

Scientific Applications:

• Structure–function mapping: Maps nearly 60% of tracked protein sequences to known 3D structures via sequence similarity searches, aiding inference of protein function.
• Interaction and mechanism analysis: Supports exploration of protein interaction networks and molecular mechanisms using mapped structures and pre-computed alignments.
• Chemical–structural integration: Enables integration of small-molecule information from PubChem with protein structures for chemical and structural analysis.
• Research use cases: Supports studies by structural biologists, molecular biologists, and chemists leveraging 3D structural data.

Methodology:

MMDB mirrors the Protein Data Bank (PDB); employs automated comparative analysis to generate graphical summaries of biological annotations for each 3D structure; and pre-computes structural alignments using the VAST algorithm.