Sensitive and accurate detection of distant protein homology is essential for the studies of protein structure, function and evolution. We recently developed PROCAIN, a method that is based on sequence profile comparison and involves the analysis of four signals--similarities of residue content at the profile positions combined with three types of assisting information: sequence motifs, residue conservation and predicted secondary structure. Here we present the PROCAIN web server that allows the user to submit a query sequence or multiple sequence alignment and perform the search in a profile database of choice. The output is structured similar to that of BLAST, with the list of detected homologs sorted by E-value and followed by profile-profile alignments. The front page allows the user to adjust multiple options of input processing and output formatting, as well as search settings, including the relative weights assigned to the three types of assisting information.
Availability: http://prodata.swmed.edu/procain/.