Name: bbcontacts
Owner: Söding Lab
Description: Prediction of beta-strand pairing from direct coupling patterns
Created: 2015-05-04 12:01:22.0
Updated: 2017-10-27 10:25:27.0
Pushed: 2016-08-10 12:56:03.0
Homepage: http://bioinformatics.oxfordjournals.org/content/31/11/1729
Size: 886
Language: Papyrus
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Prediction of protein beta-beta contacts at the residue level using direct coupling patterns
bbcontacts is a Python program predicting residue-level contacts between beta-strands by detecting patterns in matrices of predicted couplings. bbcontacts can make use of a secondary structure assignment or a secondary structure prediction.
To run bbcontacts, you will need
bbcontacts has been tested on Ubuntu 14.04 and Scientific Linux 6.5.
The following software is not necessary to run bbcontacts itself, but it is useful to generate input files for bbcontacts
bbcontacts is written in Python, and can be installed with a simple command. Simply clone the git repository and run
cd bbcontacts
python setup.py install
You can run bbcontacts by calling bbcontacts
from the command line.
bbcontacts is released under the GNU Affero General Public License v3 or later. See LICENSE for more details.
Usage: bbcontacts [options] couplingmatrix diversityvalue outputprefix (-d DSSPsecstructfile | -p PSIPREDsecstructfile)
To run bbcontacts for a given protein, you will need
More specifically, for bbcontacts to give the best possible result, you should ensure that
Additionally,
Here are two example command lines to run bbcontacts for the provided example:
bbcontacts example/1nz0D.mat 0.376 1nz0D -p example/1nz0D.psipred
bbcontacts example/1nz0D.mat 0.376 1nz0D -d example/1nz0D.dssp -c bbcontacts/bbcontacts.conf -s 10 -l -n 1nz0D
To check that the output you obtain is the same as the expected output, you can then run:
diff 1nz0D.filteredoutput.txt exampleresults/
diff 1nz0D.DSSP.filteredoutput.txt exampleresults/
When you run bbcontacts, you have to specify the output prefix as the third positional argument. Several output files will be generated:
Note: if the output file already exists, then the new output will be appended at the end of the file.
Note: If no pattern is detected above the Viterbi score thresholds specified in the configuration file, the output file contains only one line where all output values are NA.
If you use bbcontacts, please cite:
J. Andreani and J. Soeding (2015) “bbcontacts: prediction of beta-strand pairing from direct coupling patterns”, Bioinformatics. doi:10.1093/bioinformatics/btv041
[1] M. Remmert, A. Biegert, A. Hauser and J. Soeding (2012) HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nature Methods, 9, 173-175.
[2] S. Seemayer, M. Gruber and J. Soeding (2014) CCMpred — fast and precise prediction of protein residue-residue contacts from correlated mutations. Bioinformatics, doi: 10.1093/bioinformatics/btu500.
[3] W. Kabsch and C. Sander (1983). Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.
[4] D. T. Jones (1999). Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol., 292, 195-202.
[5] J. Cheng and P. Baldi (2005). Three-stage prediction of protein beta-sheets by neural networks, alignments and graph algorithms. Bioinformatics, 21 Suppl 1, 75-84. Link to the BetaSheet916 dataset file (last accessed 12 September 2014)
[6] C. Savojardo, P. Fariselli, P. L. Martelli and R. Casadio (2013). BCov: a method for predicting beta-sheet topology using sparse inverse covariance estimation and integer programming. Bioinformatics, 29, 3151-3157. Link to the BetaSheet1452 dataset file (last accessed 12 September 2014)