concavity

predictor of protein ligand binding sites from structure and conservation

ConCavity predicts protein ligand binding sites by combining evolutionary sequence conservation and 3D structure. ConCavity takes as input a PDB format protein structure and optionally files that characterize the evolutionary sequence conservation of the chains in the structure file. The following result files are produced by default: * Residue ligand binding predictions for each chain (*.scores). * Residue ligand binding predictions in a PDB format file (residue scores placed in the temp. factor field, *_residue.pdb). * Pocket prediction locations in a DX format file (*.dx). * PyMOL script to visualize the predictions (*.pml). ConCavity has many features. The default run of concavity is equivalent to ConCavity^L in the paper: 'Capra JA, Laskowski RA, Thornton JM, Singh M, and Funkhouser TA(2009) Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure. PLoS Comput Biol, 5(12).'. score_conservation(1) from the conservation-code package can be used to calculate evolutionary sequence conservation for concavity.

concavity-dbg

predictor of protein ligand binding sites (debug)

ConCavity predicts protein ligand binding sites by combining evolutionary sequence conservation and 3D structure. This package contains the debugging symbols.