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Useful interface predictors for HADDOCK

Interface predictors



  • Protein-peptide interface predictors


CPORT (protein-protein interface predictor)

CPORT is a web server for the prediction of protein-protein interfaces. It requires the protein structure coordinates (PDB format) and optional sequence alignment as input.   

CPORT is an algorithm for the prediction of protein-protein interface residues. It combines six interface prediction methods into a consensus predictor. CPORT predictions can be used as active and passive residues in HADDOCK.

Citation: de Vries SJ, Bonvin AMJJ (2011). CPORT: A Consensus Interface Predictor and Its Performance in Prediction-Driven Docking with HADDOCK. PLoS ONE 6(3): e17695. doi:10.1371/journal.pone.0017695

Web server URL: http://haddock.chem.uu.nl/services/CPORT

WHISCY (protein-protein interface predictor)

WHISCY is a program to predict protein-protein interfaces. It is primarily based on conservation, but it also takes into account structural information. A sequence alignment is used to calculate a prediction score for each surface residue of your protein.

Citation: de Vries SJ, van Dijk ADJ, Bonvin AMJJ (2006). WHISCY: WHat Information does Surface Conservation Yield? Application to data-driven docking. Proteins: Struc. Funct. & Bioinformatics, 63, 479-489. doi:10.1002/prot.20842

Web server URL: http://nmr.chem.uu.nl/whiscy


DISPLAR (protein-DNA interface predictor)

DISPLAR is a web server for the prediction of DNA binding interfaces on proteins using the protein structure coordinates (PDB format) as input.

DISPLAR is a neural network method. Given the structure of a protein known to bind DNA, the method predicts residues that contact DNA. 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-DNA complexes. On our test set, DISPLAR shows prediction accuracy over 80% and coverage of over 60% of actual DNA-contacting residues.

Citation: Tjong , H. and Zhou, H.-X. (2007). DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces. Nucl. Acids Res. 35:1465-1477.

Web server URL: http://pipe.scs.fsu.edu/displar.html


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"The FP7 WeNMR (project# 261572), H2020 West-Life (project# 675858) and the EOSC-hub (project# 777536) European e-Infrastructure projects are acknowledged for the use of their web portals, which make use of the EGI infrastructure with the dedicated support of CESNET-MetaCloud, INFN-PADOVA, NCG-INGRID-PT, TW-NCHC, SURFsara and NIKHEF, and the additional support of the national GRID Initiatives of Belgium, France, Italy, Germany, the Netherlands, Poland, Portugal, Spain, UK, Taiwan and the US Open Science Grid."
And the following article describing the WeNMR portals should be cited:
Wassenaar et al. (2012). WeNMR: Structural Biology on the Grid.J. Grid. Comp., 10:743-767.


The WeNMR Virtual Research Community has been the first to be officially recognized by the EGI.

European Union

WeNMR is an e-Infrastructure project funded under the 7th framework of the EU. Contract no. 261572

WestLife, the follow up project of WeNMR is a Virtual Research Environment e-Infrastructure project funded under Horizon 2020. Contract no. 675858