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.

Sequence size for each protein is limited to 300 residues. Longer sequences will be truncated to this length.

Enter your first protein sequence below in plain text (FASTA format; No header) Enter your second protein sequence below in plain text (FASTA format; No header)

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@nibio.go.jp

Funding

This web server has been partially funded by Grants-in-aid (Kaken-hi) to Shandar, which is thankfully acknowledged.