concavity
predictor of protein ligand binding sites from structure and conservation
Install
- All systems
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curl cmd.cat/concavity.sh
- Debian
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apt-get install concavity - Ubuntu
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apt-get install concavity - Kali Linux
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apt-get install concavity - Windows (WSL2)
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sudo apt-get updatesudo apt-get install concavity - Raspbian
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apt-get install concavity
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.