This web server takes fasta sequences of two proteins and predicts pairs of interacting residues between them. The input is a pair of amino acid sequences in the fasta format.
New (August 2026): Now you can obtain multiple grahical outputs of PPIPP web server, starting from your own PSSM files.
Click here to upload PSSM files to get PPIPP graphical outputs for multiple pairs. The server can handle multiple PSSM files and give you pairwise PPIPP predictions from a set provided by you. In order to use that feature, please use Batch Mode of the following link. Graphics rich and bulk mode options are available here
Basic sequence-pair to PPIPP prediction is provided in the following interface.
Sequence size for each protein is limited to 300 residues. Longer sequences will be truncated to this length.
Test Sequence
Copy and paste full or part of the following sequences into the text boxes above and press the predict button to test this web server.
DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVV FQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIIT GEATQEDYYTGDHYATFSLIDQTC
KKAVINGEQIRSISDLHQTLKKELALPEYYGENLDA LWDCLTGWVEYPLVLEWRQFEQSKQLTENGAESVLQ VFREAKAEGCDITIILS
Menu
(Some links are under construction)- Introduction
- Sample Output
- Expected Server Performance (for pair or single chain prediction; benchmarked over all dimer pairs)
- Expected Server Performance (for single residue prediction; benchmarked over multimers, contacts with any chain)
- Expected Server Performance (for single residue prediction; benchmarked over multimers, contacts with any chain)
- Datasets (PDB IDs) used in training
Citation
Partner-aware prediction of interacting residues in protein-protein complexes from sequence data, Ahmad S and Mizuguchi K, PLoS One (2011) 6(12)e29104 Read it here
Contact:
Shandar Ahmad
shandar@sciwhylab.org