Supplement for manuscript entitled "A critical comparative assessment of predictions of protein binding sites for biologically relevant organic compounds"

 
This web page provides datasets and links to binding site predictors associated with


Chen K, Mizianty MJ, Gao J, and Kurgan LA, 2011. A Critical Comparative Assessment of Predictions of Protein Binding Sites for Biologically Relevant Organic Compounds. Structure, 19(5):613-621

  1. Datasets
    Full dataset
    Subset with holo structures
    Subset with apo structures
    The above datasets are compressed using zip format.

  2. Links to binding site predictors
     
    ConCavity
    Capra JA, Laskowski RA, Thornton JM, Singh M, Funkhouser TA (2009) Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure. PLos Comput Biology, 5, 12
     
    MetaPocket
    Huang B. (2009) MetaPocket: a meta approach to improve protein ligand binding site prediction. Omics, 13, 325-330
     
    Fpocket
    Le Guilloux V, Schmidtke P, Tuffery P. (2009) Fpocket: an open source platform for ligand pocket detection. BMC Bioinformatics, 10, 168
     
    Findsite
    Brylinski M, Skolnick J. (2008) A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation. Proceeding of National Academy of Sciences USA, 105, 129-34
     
    PocketPicker
    Weisel M, Proschak E, Schneider G. (2007) PocketPicker: analysis of ligand binding-sites with shape descriptors. Chemistry Central Journal, 1, 7
     
    LIGSITEcsc
    Huang B, Schroeder M. (2006) LIGSITEcsc: Predict protein binding sites using the Connolly surface and degree of conservation. BMC Structural Biology, 6:19
     
    Q-siteFinder
    Laurie AT, Jackson RM. (2005) Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites. Bioinformatics, 21, 1908-169
     
    PASS
    Brady GP, Stouten P. (2000) Fast prediction and visualization of protein binding pockets with PASS. Journal of Computer-Aided Molecular Design, 14, 383-401
     
    PocketFinder
    Pocket-Finder is based on the Ligsite algorithm. Hendlich M, Rippmann F, Barnickel G. (1997) LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins. Journal of Molecular Graphics and Modeling, 15, 359-63
     
    SURFNET
    Laskowski RA. (1995) SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions. Journal of Molecular Graphics, 13, 323-30