How To Use the Molecular Modeling Database (MMDB)

How to use the Molecular Modeling Database (MMDB) and related resources: examples

 

 

Retrieve specific subsets of resolved structures

• Find structures for a gene/protein product of interest.
• Find 3D structures bound to a specific chemical (e.g., aspirin).
• Find 3D structures bound to a specific small biopolymer (e.g., a peptide).
• Retrieve 3D structures for a specific type of molecule, such as protein, RNA, DNA, protein+chemical, etc.
• Retrieve all structures from a particular source organism or taxon.

Find structural templates for proteins

• Align a query protein to a similar sequence from a 3D structure and interactively view sequence/structure relationships.

Find structures that are similar in 3D shape (using VAST)

• Find structures with similarly shaped proteins or 3D domains, regardless of their degree of sequence similarity. [VAST]
• Find structures with similarly shaped biological assemblies, regardless of their degree of sequence similarity. [VAST+]
• Compare a newly resolved 3D structure in PDB format against the 3D coordinates of known structures already in the public domain. [VAST Search]

View 3D structures

• Interactively view a 3D structure and its corresponding sequence data to examine sequence-structure relationship.
• Identify putative active site residues.