Database of Structural Motifs in Proteins (DSMP)

This database is primarily based on the results of the PROMOTIF program. It contains information on eleven well-characterized structural motifs, and one on the coils in proteins that we have developed. The individual motifs are characterized by different fields (as in PROMOTIF) that describe them. Each motif contains a particular type of information, i.e., PDB entry, chain, protein name, geometrical parameters, amino acid sequence, motif type, location along the sequence, etc. One can query the database by specifying a particular amino acid sequence, in order to retrieve all entries characterized by the sequence along with the associated details for each ‘hit’ in the PDB. The database can be queried on each of the fields defined for a particular motif or a combination of the fields. We have recently included the domain information by referring to the CATH database. This is useful to identify, not only, helices characterized by a particular sequence along with the associated details for the helix motif, but also the domains in which these helices are observed. This provides a higher level of hierarchical association concerning sequence-structure relatedness in proteins.