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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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