Database Commons a catalog of biological databases

Database Commons - MMDB

MMDB

Citations: 79

z-index 4.61

Short name MMDB
Full name Macromolecular Database
Description Three dimensional structures provide a wealth of information on the biological function and the evolutionary history of macromolecules. They can be used to examine sequence-structure-function relationships, interactions, active sites, and more.
URL http://www.ncbi.nlm.nih.gov/structure
Year founded 2012
Last update & version 2011-11-30    v1.0
Availability Free to all users
University/Institution hosted National Center for Biotechnology Information
Address Bldg. 38 A,Room 8N805,8600 Rockville Pike,Bethesda,MD 20894,USA
City Bethesda
Province/State MD
Country/Region United States
Contact name Thomas Madej
Contact email madej@ncbi.nlm.nih.gov
Data type(s)
Major organism(s)
Keyword(s)
  • three-dimensional structure
Publication(s)
  • MMDB: 3D structures and macromolecular interactions. [PMID: 22135289]

    Thomas Madej, Kenneth J Addess, Jessica H Fong, Lewis Y Geer, Renata C Geer, Christopher J Lanczycki, Chunlei Liu, Shennan Lu, Aron Marchler-Bauer, Anna R Panchenko, Jie Chen, Paul A Thiessen, Yanli Wang, Dachuan Zhang, Stephen H Bryant
    Nucleic acids research 2012:40(Database issue)
    79 Citations (Google Scholar as of 2016-05-02)

    Abstract: Close to 60% of protein sequences tracked in comprehensive databases can be mapped to a known three-dimensional (3D) structure by standard sequence similarity searches. Potentially, a great deal can be learned about proteins or protein families of interest from considering 3D structure, and to this day 3D structure data may remain an underutilized resource. Here we present enhancements in the Molecular Modeling Database (MMDB) and its data presentation, specifically pertaining to biologically relevant complexes and molecular interactions. MMDB is tightly integrated with NCBI's Entrez search and retrieval system, and mirrors the contents of the Protein Data Bank. It links protein 3D structure data with sequence data, sequence classification resources and PubChem, a repository of small-molecule chemical structures and their biological activities, facilitating access to 3D structure data not only for structural biologists, but also for molecular biologists and chemists. MMDB provides a complete set of detailed and pre-computed structural alignments obtained with the VAST algorithm, and provides visualization tools for 3D structure and structure/sequence alignment via the molecular graphics viewer Cn3D. MMDB can be accessed at http://www.ncbi.nlm.nih.gov/structure.

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Tags

DNA Protein Structure
three-dimensional structure

Record metadata

  • Created on: 2015-06-20
  • Curated by:
    • Lin Liu [2016-04-11]
    • Lin Liu [2016-03-26]
    • Li Yang [2015-06-26]
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