PPIK, The Protein-Protein Interface Key Residue Prediction Server

This server can be used to predict the protein-protein interface residues for a given protein chain, which is summarized on this page. For your target protein complete the following steps to receive a prediction of the protein-binding residues for your protein chain. (Note: Currently we are taking only single chain PDB structures).

The button below automatically loads the data needed to do a PPIK binding residue prediction for 1FKS, chain A, or if you wish you can just look at the output that was given from a saved prediction we did earlier for 1FKS chain A. After clicking the button it may take up to ten seconds for the data to be downloaded and for the prediction to start, and it will finish in around 5 minutes.

Output from a previous prediction on chain A from 1FKS can be found here.

PLease provide the protein chain using either option A or option B (Help)
Option A) For single protein chain structures that are to be uploaded from text files.
Step A1: Upload the structure of your target protein with standard PDB file format. (Example)
Step A2: Upload the prepared evolution information of your target protein in ConSurf format, if available. (Example)

Option B) For known PDB archive entries with multiple protein chains The server will check for and retrieve the ConSurf data information automatically if it has been precalculated in the ConSurf-DB; if it has not, it will attempt to generate the ConSurf data automatically. If no ConSurf data can be generated, the prediction will continue and you will be informed of the missing ConSurf data on the Results page.
Step B1: Enter the PDB ID code. E.g. 1fks
Step B2: Enter the chain assignment letter. E.g. A

Submission
Optional Step: Optional: If you would like an email saying when your results are ready please enter an email address, however you do not have to enter anything here.
Submission Step: Click on the submit button to send to the protein interface residue prediction server, it may take 10 seconds while we check your input. Results will be kept for 2 months. (Help)
Multiple Submissions: You may use the multiple prediction submission form for predictions on many different single chains.

References and programs used in creating this server.

If you use PPIK for predicting binding residues please cite
PPIK: Detecting protein-protein interface key residues, Yao-Chi Chen, Yu-Hsien Chen, Jon D. Wright,` Yi-Shiuian Huang and Carmay Lim.

PPIK relies on the following software to make predictions.

AMBER: D.A. Case, T.A. Darden, T.E. Cheatham, III, C.L. Simmerling, J. Wang, R.E. Duke, R. Luo, R.C. Walker, W. Zhang, K.M. Merz, B. Roberts, S. Hayik, A. Roitberg, G. Seabra, J. Swails, A.W. Götz, I. Kolossváry, K.F. Wong, F. Paesani, J. Vanicek, R.M. Wolf, J. Liu, X. Wu, S.R. Brozell, T. Steinbrecher, H. Gohlke, Q. Cai, X. Ye, J. Wang, M.-J. Hsieh, G. Cui, D.R. Roe, D.H. Mathews, M.G. Seetin, R. Salomon-Ferrer, C. Sagui, V. Babin, T. Luchko, S. Gusarov, A. Kovalenko, and P.A. Kollman (2012), AMBER 12, University of California, San Francisco. PubMed

CONSURF & CONSURF-DB ConSurf: Using Evolutionary Data to Raise Testable Hypotheses about Protein Function. Celniker G., Nimrod G., Ashkenazy H., Glaser F., Martz E., Mayrose I., Pupko T., and Ben-Tal N. (2013) Isr. J. Chem. March 10, doi: 10.1002/ijch.201200096
ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Ashkenazy H., Erez E., Martz E., Pupko T. and Ben-Tal N. (2010) Nucleic Acids Research, 38, W529-533. PubMed
The ConSurf-DB: Pre-calculated evolutionary conservation profiles of protein structures. Goldenberg O., Erez E., Nimrod G and. Ben-Tal N. (2009) Nucleic Acids Research, 37, Database issue D323-D327. PubMed

PDB2PQR PDB2PQR: an automated pipeline for the setup of Poisson–Boltzmann electrostatics calculations . Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. (2004) Nucleic Acids Research, 32, W665-W667. PubMed

NACCESSS NACCESS - Accessibility calculations. Hubbard S.J. and Thornton J.M. (1993). Department of Biochemistry and Molecular Biology, University College London, NACCESS

JSmol JSmol: an open-source HTML5 viewer for chemical structures in 3D. Homepage

PPIK is hosted at The Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan.

PPIK, The Protein-Protein Interface Key Residue Prediction Server

PLease provide the protein chain using either option A or option B (Help)

Option A) For single protein chain structures that are to be uploaded from text files.

Option B) For known PDB archive entries with multiple protein chains

Submission

References and programs used in creating this server.