a server for the analysis, comparison and ranking of docking models based on inter-residue contacts

The renumbering tool first extracts the FASTA sequences from the PDB files, then uses BLASTclust (ftp://ftp.ncbi.nih.gov/blast/documents/blastclust.html) to clusterize them and aligns sequences within each cluster with ClustalW (http://www.ebi.ac.uk/Tools/msa/clustalw2/), finally it rewrites the PDB files to have the sequences consistently renumbered. Please note that this may take several hours, depending on the length and especially number of the input PDB files. Therefore, please insert your e-mail address to be notified when the job is done.

The sequence identity and coverage to be used in BLASTclust can be set by the user (default values are 90% and .9, respectively). The expected number of different sequences can also be optionally specified (e.g. “2” for an heterodimer, “1” for an homodimer).