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-   -   Bug#689020: ITP: concavity -- predictor of protein ligand binding sites from 3D structure and sequence conservation (http://www.linux-archive.org/debian-development/708068-bug-689020-itp-concavity-predictor-protein-ligand-binding-sites-3d-structure-sequence-conservation.html)

Laszlo Kajan 09-28-2012 10:39 AM

Bug#689020: ITP: concavity -- predictor of protein ligand binding sites from 3D structure and sequence conservation
 
Package: wnpp
Severity: wishlist
Owner: Laszlo Kajan <lkajan@rostlab.org>

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* Package name : concavity
Version : 0.1
Upstream Author : Thomas Funkhouser <funk@CS.Princeton.EDU>, John A. Capra <tonyc@cs.princeton.edu>
* URL : http://compbio.cs.princeton.edu/concavity/
* License : GPL-3+
Programming Lang: C++
Description : predictor of protein ligand binding sites from 3D structure and sequence 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).'.

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