GSATools

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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.




Download
Source Code
Source code compatible with GROMACS 4.0.x:
gsatools-4.0.x-1.00.tar.gz
Source code compatible with GROMACS 4.5.x:
gsatools-4.5.x-1.00.tar.gz


Precompiled binaries
Binaries compiled with GROMACS 4.0.7 on Linux x86-64
g_sa_encode_407_lnx
g_sa_analyze_407_lnx
Binaries compiled with GROMACS 4.0.7 on Mac OS X 10.8
g_sa_encode_407_osx
g_sa_analyze_407_osx
Binaries compiled with GROMACS 4.5.5 on Linux x86-64
g_sa_encode_455_lnx
g_sa_analyze_455_lnx
Binaries compiled with GROMACS 4.5.5 on Mac OS X 10.8
g_sa_encode_455_osx
g_sa_analyze_455_osx


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.


Install
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.
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 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.
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.




References
  • 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




Authors

Alessandro Pandini, Arianna Fornili, Franca Fraternali and Jens Kleinjung

Contacts

email developer