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Analysis of allosteric communication and functional local motions using a structural alphabet http://jkleinj.github.io/GSAtools/
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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/>.