Improved Searching with New Sequence Identity Cutoff
A sequence identity cutoff value option has been added to Advanced Search for "Sequence (BLAST/FASTA/PSI-BLAST)".
To use this feature, enter a sequence by typing a PDB ID in the Structure ID text box and selecting a Chain ID from the pull-down menu or by pasting a sequence into the Sequence text box.
Using the Sequence Identity Cutoff (a percentage value between 0 and 100) option, the results returned will have at least the specified sequence identity to the target sequence. For example, entering 100% returns entries with exactly match the same sequence. As many structures have low E-values but only a few have high sequence identity with the target sequence, fewer results will be returned when using this feature.
The % sequence identity can be seen by displaying the sequence alignment on the query results page. All results returned will have sequence identity greater than or equal to the cutoff used.
This Sequence Identity Cutoff differs from the 'retrieve representatives' option found at the bottom of the Advanced Search screen and on the Query Results pages. The option to "retrieve only representatives at XX% sequence identity utilizes RCSB PDB's use of BLAST clustering to remove redundant sequences, and returns one representative per cluster.