Concavity
Concavity
http://compbio.cs.princeton.edu/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.
Licensing
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License:
Permission to use, copy, modify and distribute this software and its documentation for any purpose is hereby granted without fee, provided that the above copyright notice and this permission notice appear in all copies of this software and that you do not sell the software.
THE SOFTWARE IS PROVIDED "AS IS" AND WITHOUT WARRANTY OF ANY KIND, EXPRESS, IMPLIED OR OTHERWISE, INCLUDING WITHOUT LIMITATION, ANY WARRANTY OF MERCHANTABILITY OR FITNESS FOR A
PARTICULAR PURPOSE.License
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Debian
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20 March 2013
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License: GPL-3.0+
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This package is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
On Debian systems, the complete text of the GNU General Public License version 3 can be found in "/usr/share/common-
licenses/GPL-3".
Leaders and contributors
| Contact(s) | Role |
|---|---|
| Thomas Funkhouser | contact |
Resources and communication
| Audience | Resource type | URI |
|---|---|---|
| Download | http://compbio.cs.princeton.edu/concavity/ | |
| Debian (Ref) | https://tracker.debian.org/pkg/concavity |
Software prerequisites
Permission is granted to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License, Version 1.3 or any later version published by the Free Software Foundation; with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts. A copy of the license is included in the page “GNU Free Documentation License”.
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