3D Macromolecular Structures

There are several ways to search the Molecular Modeling Database (MMDB):

  text term search Use the query box above or the Entrez Structure page to search the Molecular Modeling Database (MMDB) by key word (e.g., tumor suppressor), accession number, author name, journal name, and more. The MMDB help document provides search tips.  
  protein sequence query Use protein BLAST to compare a query protein sequence against the protein sequences extracted from PDB 3-dimensional structure records. If your query protein sequence already exists in the Entrez Protein database, precalculated BLAST results are instantly available by opening the Links menu for your protein sequence of interest and selecting Related Structures (see frame B of illustrated example). This will retrieve protein structures that are sequence-similar to your query.
  3D coordinates for a newly resolved structure Use the VAST Search program to upload the 3D coordinates of a newly resolved structure in PDB format and compare it against the 3D coordinates of structures already available in MMDB. This will retrieve similar 3D structures as determined by purely geometric criteria, regardless of the level of sequence similarity. You can then use the free Cn3D program to view the similar structures superposed on your query.

If your structure is already publicly available in the Entrez Structure (MMDB) database, then you can simply enter the structure's PDB ID or MMDB ID on the VAST home page, in order to retrieve other structures that contain similarly shaped individual protein molecules or 3D domains, or on the VAST+ home page, in order to retrieve other structures that have similarly shaped biological assemblies.
  direct fetch via UID Retrieve a 3D structure record directly from the backend database by entering its unique identifier (UID), in the form of a PDB ID or MMDB ID, in the text box below:
Note: the "text term search" function also allows you to enter either of those unique identifiers (UIDs), but it first searches the Entrez indices for the UID, then retrieves the record. In contrast, the "direct fetch via UID" option bypasses the Entrez indices and simply retrieves the specified record.
  The "How To" page provides quick start guides for some common types of searches, and the MMDB Help document provides additional search tips. Once records of interest are retrieved, follow Entrez's "Links" to discover associations among previously disparate data.  
Revised 09 March 2016