Macromolecular Structures Resource Group

Molecular Modeling Database (MMDB)

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.

Retrieve by MMDB ID or PDB ID: 

 

 

iCn3D

A new WebGL-based viewer for interactive viewing of three-dimensional macromolecular structures on the web, without the need to install a separate application, and enables you to (1) interactively view 3D structures and corresponding sequence data; (2) interactively view superpositions of similar structures; (3) cutomize the display of a structure and generate a URL that allows you to share the link; (4) incorporate iCn3D into your own pages. An example of each is accessible from the "About iCn3D" page.  

 

Cn3D

A tool for visualization of three-dimensional structures, available for Mac and PC, with emphasis on interactive examination of sequence-structure relationships and superposition of geometrically similar structures. Cn3D can be used to display MMDB structures, superpositions of VAST similar structures, and conserved core motifs identified in conserved domains.  

 

Vector Alignment Search Tool (VAST)

A computer algorithm developed at NCBI and used to identify similar protein 3-dimensional structures by purely geometric criteria, and to identify distant homologs that cannot be recognized by sequence comparison. "Similar structures" for every structure in MMDB are pre-computed using VAST and accessible via links on the MMDB Structure Summary pages. The VAST Search web service also allows you to compare the coordinates of a newly resolved structure in PDB file format against all structures in MMDB to find its neighbors.  

 

Vector Alignment Search Tool Plus (VAST+)

A tool designed to identify macromolecules that have similar 3-dimensional structures, with an emphasis on finding those with similar biological assemblies ("biological units" or "biounits"). The similarities are calculated using purely geometric criteria, and therefore can identify distant homologs that cannot be recognized by sequence comparison. VAST+ is built upon the original Vector Alignment Search Tool (VAST), and expands the capabilities of that program by making it possible to now find macromolecular structures that have similarly shaped biological units, not just those that share similarly shaped individual protein molecules or fragments.  

 

 

Retrieve structures for a gene/protein product of interest

 

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

 

Retrieve 3D structures bound to a specific chemical (e.g., aspirin)

 

Interactively view a 3D structure and its corresponding sequence data to examine sequence-structure relationship

 

Find protein structures that are similar in 3D shape to a structure of interest, regardless of degree of sequence similarity

 

Compare a newly resolved 3D structure in PDB format against the 3D coordinates of known structures already in the public domain

 

  SEE ALL "HOW TO"  >>

   Protein Only   DNA Only   RNA Only   

   Protein+Chemical   DNA+Chemical   RNA+Chemical   

   Protein+DNA   Protein+RNA   DNA+RNA   

     

  The "How To" page provides tips for searching by molecule type, gene/protein product, and more. You can also retrieve any search set above and then add terms of interest to the query box. For example, try this: (a) follow the link for "Protein + Chemical"; (b) insert AND neurofibromin in the query box at the top of the search results page; and (c) press "Go" to retrieve neurofibromin protein structures bound to a chemical.