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BioCodeKb - Bioinformatics Knowledgebase

The Molecular Modeling Database (MMDB) helps in access to structure data by connecting them with associated literature, protein and nucleic acid sequences, chemicals, biomolecular interactions, and more. It works as a part of Entrez.

The goal of Entrez's 3D-structure database is to make structure information and the functional annotation it can provide easily accessible to molecular biologists. Entrez's CDD defines protein domains as recurrent evolutionary modules.

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 that is 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 through the molecular graphics viewer Cn3D.

The Molecular Modeling Database (MMDB) contains 3D macromolecular structures, including proteins and polynucleotides. MMDB contains over 28,000 structures and is linked to the rest of the NCBI databases, including sequences, bibliographic citations, taxonomic classifications, and sequence and structure neighbors. Entrez is the integrated, text-based search and retrieval system used at NCBI for the major databases, including PubMed, Nucleotide and Protein Sequences, Protein Structures, Complete Genomes, Taxonomy, and others. Experimentally resolved structures of proteins, RNA, and DNA, derived from the Protein Data Bank (PDB), with value-added features such as explicit chemical graphs, computationally identified 3D domains (compact substructures) that are used to identify similar 3D structures, as well as links to literature, similar sequences, information about chemicals bound to the structures, and more. These connections make it possible, for example, to find 3D structures for homologs of a protein sequence of interest, then interactively view the sequence-structure relationships, active sites, bound chemicals, journal articles, and more.

The structure summary pages of MMDB provides a molecular graphics thumbnail which shows the view of the biological unit.

Three-dimensional structures are now known within most protein families and it is likely, when searching a sequence database, that one will identify a homolog of known structure. Entrez's Molecular Modeling Database (MMDB) provides graphical summaries of the biological annotation available for each 3D structure, based on the results of automated comparative analysis.


  • Facilitates computation on 3D structure data

  • Analysis of individual structures and relationships among them

  • Biological and geometrical features within 3D structures

  • Conserved protein domain annotations

  • Evolutionary relationships among 3D structures

  • Functional relationships among 3D structures

  • Interactive views of sequence-structure relationships

  • Identify representative 3D structures for protein families

  • Examine sequence-structure-function relationships

  • View 3D structures of conserved core motifs

  • Identify putative active site residues


Need to learn more about MMDB and much more?

To learn Bioinformatics, analysis, tools, biological databases, Computational Biology, Bioinformatics Programming in Python & R through interactive video courses and tutorials, Join BioCode.

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