Analysis of allosteric communication and functional local motions using a structural alphabet
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README

GSATools project
----------------
GSAtools is a set of programs that translate ensembles of protein conformations
into alignments of structural strings using a Structural Alphabet (SA) and
perform a wide range of statistical analyses. 

References
----------
If you publish results produced with the GSATools or develop methods based on
the GSATools code, please cite the following papers:

Pandini A, Fornili A, Fraternali F, Kleinjung J.
Detection of allosteric signal transmission by information-theoretic analysis of
protein dynamics.
FASEB J. 2012 26(2):868-81.
doi: 10.1096/fj.11-190868.

Pandini A, Fornili A, Kleinjung J.
Structural alphabets derived from attractors in conformational space.
BMC Bioinformatics 2010 11:97.
doi: 10.1186/1471-2105-11-97.

Install
-------
Please read the general 'INSTALL' instructions.

Usage
-----
GSAtools has been integrated into the Gromacs environment and it uses the
standard syntax of Gromacs analysis tools. Help info for each tool can be
printed out using the --help flag, e.g.:

g_sa_encode --help

Please refer also to the examples provided in the Test suite and in the Tutorial
included in this distribution.

R scripts for the analysis and data visualisation are included in the Rscripts
directory. All the scripts can be easily modified to process user-provided data
by changing the parameters in the first section of the files.

Availability
------------
The program is made available under the GNU Public License for academic
scientific purposes and under the condition that proper acknowledgement
is made to the authors of the program in publications resulting from the use
of the program.

License
-------
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 program 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/>.