concavity binary package in Ubuntu Xenial ppc64el
ConCavity predicts protein ligand binding sites by combining evolutionary
sequence conservation and 3D structure.
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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.
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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).
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ConCavity has many features. The default run of concavity is equivalent to
ConCavity 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_
calculate evolutionary sequence conservation for concavity.
Publishing history
Date | Status | Target | Component | Section | Priority | Phased updates | Version | ||
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2016-01-08 19:38:31 UTC | Published | Ubuntu Xenial ppc64el | release | universe | science | Extra | 0.1+dfsg-1 | ||
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Deleted | Ubuntu Xenial ppc64el | proposed | universe | science | Extra | 0.1+dfsg-1 | |||
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2016-01-08 19:42:08 UTC | Superseded | Ubuntu Xenial ppc64el | release | universe | science | Extra | 0.1-2 | ||
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