Method at a Glance

cons-PPISP is a consensus neural network method for predicting protein-protein interaction sites. Given the structure of a protein, cons-PPISP will predict the residues that will likely form the binding site for another protein. The inputs to the neural network include position-specific sequence profiles and solvent accessibilities of each residue and its spatial neighbors. The neural network is trained on known structures of protein-protein complexes. On a benchmark set of 22 protein complexes, cons-PPISP shows 71% prediction accuracy and 50% coverage of actual interface residues.

  • Chen, H-L and Zhou, H-X. Prediction of interface residues in protein-protein complexes by a consensus neural network method: Test against NMR data. Proteins 61:21-35 (2005).
  • Zhou, H.-X. and Shan, Y. Prediction of protein interaction sites from sequence profiles and residue neighbor list. Proteins 44:336-343 (2001).

  Note: The size of protein can be submitted here is from 40 to 2000 residues.

Predict binding site for your protein here

If you have more than a few proteins and would like to run cons-PPISP in batch mode, click here.

  • Type an arbitrary name for referencing your submission:
  • Enter your email address, where the prediction will be sent to:
  • Enter the chain(s) of your protein:
    No chain ID: leave underscore ("_") alone
    Single chain: delete "_" and type letter or number for chain ID, e.g., A
    Multiple chains: delete "_" and type chain IDs separated by comma without space, e.g., A,B,C
  • Upload your PDB file:

    OR paste your pdb (do NOT do both):

  • Note: cons-PPISP is a 3D structure based predictor, not a sequence based.

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