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 - Dockerfile
- dockerfile.run/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.