concavity 0.1-2~ubuntu12.04.1 source package in Ubuntu
Changelog
concavity (0.1-2~ubuntu12.04.1) precise-backports; urgency=low * No-change backport to precise (LP: #1165011) -- Felix Geyer <email address hidden> Sun, 28 Apr 2013 19:51:41 +0200
Upload details
- Uploaded by:
- Felix Geyer
- Uploaded to:
- Precise
- Original maintainer:
- Debian Med
- Architectures:
- any
- Section:
- science
- Urgency:
- Low Urgency
See full publishing history Publishing
| Series | Published | Component | Section | |
|---|---|---|---|---|
| Precise | backports | universe | science |
Downloads
| File | Size | SHA-256 Checksum |
|---|---|---|
| concavity_0.1.orig.tar.xz | 314.6 KiB | d139ad02edfedf5199432e34da1dc2be91004bcad650f30c03a69d21c9ab9f79 |
| concavity_0.1-2~ubuntu12.04.1.debian.tar.gz | 10.8 KiB | 84ba7f0f76853aaa95c6b7f4ca193d74b6b09a15c9c330fdf31cf5793fd0c6de |
| concavity_0.1-2~ubuntu12.04.1.dsc | 2.0 KiB | 3c30321f8878b5935a2d312302185544118d96a1843ccddefbefa23a15c4f1ac |
Available diffs
Binary packages built by this source
- 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.
