In this section users can provide a PDB entry and its chain to search for chains with similar sequence in the PDB.

PDB id: the identifier of PDB entry to search for.

Chain: a chain from PDB id informed in the previous text box.

Sequence identity cutoff (%): minimum sequence similarity threshold that a chain should have to be recovered.

By clicking on More options , users are able to set three additional parameters.

Search tool: the sequence alignment algorithm, which can be BLAST, FASTA or PSI-BLAST, used to perform the search. The default is Blast.

Mask low complexity: masks low complexity regions in a sequence to avoid spurious alignments. Low complexity regions in the sequence are displayed as X in the query sequence. The default is yes.

E-value cutoff: describes the number of hits one can "expect" to see by chance when searching a database of a particular size. The lower the E-value, or the closer it is to zero, the more "significant" the match is. The default is 10.0. For details, please refer to http://www.ncbi.nlm.nih.gov/BLAST/tutorial/Altschul-1.html.