MESSAGE: Please read (25/01/2010)
There have been problems with the PDB update on our server this month which means that some structures will not be accepted. Sorry for any inconvenience, we hope to have PPI-Pred fully working within 10 days.
Instructions
1. Select from one of two prediction modes:
a. "Protein": Protein-protein binding site prediction.
b. "DNA": DNA binding site prediction.
2. Specify chain identifier (column 22 of ATOM records in the PDB file) of protein.
3. Submit a protein structure for analysis in one of four ways:
a. Enter four letter PDB code (public domain PDB files only).
b. Upload PDB file (public domain or user-defined PDB file).
c. Copy and paste contents of any PDB file into a text box.
d. Batch processing.
Note on NMR structures: PPI-Pred can only process SINGLE models, please edit the PDB file accordingly.
Updates
30/11/2009: Due to problems with the mail server, email notification has been disabled. Sorry for any inconvenience.
09/09/2005: Previously, in cases where a query protein has no known homologs, the error message "Pir File Could Not Be Opened" appeared. PPI-Pred can now process such proteins successfully by assigning a conservation score of 0.5 to each residue thus negating the influence of the conservation attributes on the SVM prediction.
12/09/2005: Batch processing is now possible.
Troubleshooting
If any problems are encountered whilst using PPI-Pred, do not hesitate to email James Bradford (J.R.Bradford@leeds.ac.uk) with details on the nature of the problem and the PDB file submitted.
