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.