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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. The software has been integrated into the GROMACS environment.

Source Code
Source code compatible with GROMACS 4.0.x:
Source code compatible with GROMACS 4.5.x:

Precompiled binaries
Binaries compiled with GROMACS 4.0.7 on Linux x86-64
Binaries compiled with GROMACS 4.0.7 on Mac OS X 10.8
Binaries compiled with GROMACS 4.5.5 on Linux x86-64
Binaries compiled with GROMACS 4.5.5 on Mac OS X 10.8

The requirements to use the precompiled binaries are: GNU Scientific Library (GSL) installed on the system and a working installation of GROMACS.
Before using these binaries, it is advisable to run the script GMXRC to set the required environment variables and then to directly set the environment variable GMXLIB to $GMXDATA/gromacs/top. The GMXRC file is included in the bin directory of GROMACS installation.

Please read the instructions in the INSTALL file included in the distribution.
GROMACS should have been compiled as a set of shared libraries (--enable-shared) in single precision and in serial mode, i.e. without using MPI. GSATools is currently not implemented to work with a parallel version of GROMACS. Future versions will include full compatibility.
If you installed the GNU Scientific Library (GSL) for Linux using your distribution package manager, please check to have installed both gsl and gsl-dev (or gsl-devel) packages.
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 the 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.
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.

  • Pandini A, Fornili A, Fraternali F, Kleinjung J - GSATools: analysis of allosteric communication and functional local motions using a Structural Alphabet
    Bioinformatics 29(16):2053-2055, 2013
    PubMed URL
  • Pandini A, Fornili A, Fraternali F, Kleinjung J - Detection of allosteric signal transmission by information-theoretic analysis of protein dynamics
    The FASEB Journal 26(2):868-881, 2012
    PubMed URL
  • Pandini A, Fornili A, Kleinjung J - Structural alphabets derived from attractors in conformational space
    BMC Bioinformatics 11(1):97, 2010
    PubMed URL Data


Alessandro Pandini, Arianna Fornili, Franca Fraternali and Jens Kleinjung


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