Bioinformatics Bioinformatics File Formats

MMDB Format

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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 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.

Significant limitations of the PDB format have allowed the development of new formats to handle increasingly complicated structure data. The most popular new formats include the macromolecular crystallographic information file (mmCIF) and the molecular modeling database (MMDB) file. Both formats are highly explained by computer software, meaning that information in each field of a record can be retrieved separately. These new formats facilitate the retrieval and organization of information from database structures.

A new format is the MMDB format developed by the NCBI to parse and sort pieces of information in PDB. The objective is to allow the information to be more easily integrated with GenBank and Medline through Entrez.

An MMDB file is written in the ASN.1 format, which has information in a record structured as a nested hierarchy. This allows faster retrieval than mmCIF and PDB. Furthermore, the MMDB format includes bond connectivity information for each molecule, called a “chemical graph,” which is recorded in the ASN.1 file. The inclusion of the connectivity data allows easier drawing of structures.

The solved structures are deposited in PDB, which uses a PDB format to describe structural details. However, the original PDB format has limited capacity and is difficult to be parsed by computer software.

To overcome the limitations of PDB format, new formats such as mmCIF and MMDB have been developed. MMDB databases are self-contained “search tree indexed files” so we cannot just sequentially read and display the file record by record (even its “data records” include pointers to other “cache” data records that contain the actual human readable strings such as country name).

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