Learn to use Molecular Modeling Database, or MMDB , which is Entrez's structural database brought to you by the National Institutes of Health and the National Center for Biotechnology Information. It contains an extensive collection of three-dimensional structures with detailed annotation that can be used to learn about the structure and function of many proteins. MMDB's structures were originally obtained from PBD and they contain descriptions, references and extensive multi-directional links both inside and outside of the NCBI network. There are pre-computed structural homologs, i.e. related structures or neighbors, that you can access, and extensive visualization and comparative analysis tools that you can use to examine individual structures, or multiple structures aligned.

You will learn:

  • to search MMDB using both basic and advanced query techniques
  • how to understand the detailed results you obtain
  • methods to visualize and manipulate structures using NCBIs Cn3D structural viewer
  • to locate and view structurally aligned homologs


This tutorial is a part of the tutorial group Protein-centric and protein structure resources. You might find the other tutorials in the group interesting:

Pfam: Protein Domain families

UniProt: UniProt, Universal Protein Resource

RCSB PDB: RCSB Protein Data Bank

Entrez Protein: NCBI's Entrez Protein for amino acid-centric information

Structural Biology Knowledgebase: The Protein Structure Initiative Structural Biology Knowledgebase


Proteins : Tools that are primarily used in the storage, retrieval, or exploration of amino acid based data. Some tools may also involve nucleotide sequence information.

NCBI : This category includes resources maintained at the National Center for Biotechnology Information (NCBI).


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Sidhu K. Gaganpreet et al., Evolution of meiotic recombination genes in maize and teosinte Plant genomics. BMC Genomics (2017) doi:10.1186/s12864-017-3486-z

Tarr Ellen K. D. et al., Establishing a reference array for the CS-αβ superfamily of defensive peptides Evolutionary Biology. BMC Research Notes (2016) doi:10.1186/s13104-016-2291-0

Kim Sunghwan et al., Similar compounds versus similar conformers: complementarity between PubChem 2-D and 3-D neighboring sets Graphical Abstract. Journal of Cheminformatics (2016) doi:10.1186/s13321-016-0163-1

Triant A Deborah et al., Most partial domains in proteins are alignment and annotation artifacts. Genome Biology (2015) doi:10.1186/s13059-015-0656-7

Jin Xian et al., PDB-Explorer: a web-based interactive map of the protein data bank in shape space Structural analysis Graphical abstract. BMC Bioinformatics (2015) doi:10.1186/s12859-015-0776-9