GSATools

 

GSATools1 is a set of programs that translate ensembles of protein conformations into alignments of structural strings using a Structural Alphabet (SA) and performs a wide range of statistical analyses1-3. The software has been integrated into the GROMACS environment.

Download

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

 

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.

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.

References

 

1 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

 

2 Pandini A, Fornili A, Fraternali F, Kleinjung J

"Detection of allosteric signal transmission by information-theoretic analysis of protein dynamics"

FASEB J 26(2):868-81, 2012

PubMed   URL

 

3 Pandini A, Fornili A, Kleinjung J

"Structural alphabets derived from attractors in conformational space"

BMC Bioinformatics 11(1):97, 2010

PubMed   URL