GSATools: analysis of allosteric communication and functional local motions using a Structural Alphabet

Alessandro Pandini; Arianna Fornili; Franca Fraternali; Jens Kleinjung

doi:10.1093/bioinformatics/btt326

GSATools: analysis of allosteric communication and functional local motions using a Structural Alphabet

Alessandro Pandini, Arianna Fornili, Franca Fraternali, Jens Kleinjung

Research output: Contribution to journal › Article › peer-review

35 Citations (Scopus)

Abstract

MOTIVATION: GSATools is a free software package to analyse conformational ensembles and to detect functional motions in proteins by means of a Structural Alphabet. The software integrates with the widely used GROMACS simulation package and can generate a range of graphical outputs. Three applications can be supported: (i) investigation of the conformational variability of local structures; (ii) detection of allosteric communication; (iii) identification of local regions that are critical for global functional motions. These analyses provide insights into the dynamics of proteins and allow for targeted design of functional mutants in theoretical and experimental studies. AVAILABILITY: The C source code of the GSATools along with a set of pre-compiled binaries is freely available under GNU General Public License from http://mathbio.nimr.mrc.ac.uk/wiki/GSATools. CONTACT: [email protected] and [email protected]. SUPPLEMENTARY INFORMATION: A step-by-step tutorial is available in the Supplementary data at Bioinformatics online.

Original language	English
Pages (from-to)	2053-2055
Number of pages	3
Journal	Bioinformatics (Oxford, England)
Volume	29
Issue number	16
DOIs	https://doi.org/10.1093/bioinformatics/btt326
Publication status	Published - 5 Jun 2013

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title = "GSATools: analysis of allosteric communication and functional local motions using a Structural Alphabet",

abstract = "MOTIVATION: GSATools is a free software package to analyse conformational ensembles and to detect functional motions in proteins by means of a Structural Alphabet. The software integrates with the widely used GROMACS simulation package and can generate a range of graphical outputs. Three applications can be supported: (i) investigation of the conformational variability of local structures; (ii) detection of allosteric communication; (iii) identification of local regions that are critical for global functional motions. These analyses provide insights into the dynamics of proteins and allow for targeted design of functional mutants in theoretical and experimental studies. AVAILABILITY: The C source code of the GSATools along with a set of pre-compiled binaries is freely available under GNU General Public License from http://mathbio.nimr.mrc.ac.uk/wiki/GSATools. CONTACT: [email protected] and [email protected]. SUPPLEMENTARY INFORMATION: A step-by-step tutorial is available in the Supplementary data at Bioinformatics online.",

author = "Alessandro Pandini and Arianna Fornili and Franca Fraternali and Jens Kleinjung",

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T2 - analysis of allosteric communication and functional local motions using a Structural Alphabet

AU - Pandini, Alessandro

AU - Fornili, Arianna

AU - Fraternali, Franca

AU - Kleinjung, Jens

PY - 2013/6/5

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AB - MOTIVATION: GSATools is a free software package to analyse conformational ensembles and to detect functional motions in proteins by means of a Structural Alphabet. The software integrates with the widely used GROMACS simulation package and can generate a range of graphical outputs. Three applications can be supported: (i) investigation of the conformational variability of local structures; (ii) detection of allosteric communication; (iii) identification of local regions that are critical for global functional motions. These analyses provide insights into the dynamics of proteins and allow for targeted design of functional mutants in theoretical and experimental studies. AVAILABILITY: The C source code of the GSATools along with a set of pre-compiled binaries is freely available under GNU General Public License from http://mathbio.nimr.mrc.ac.uk/wiki/GSATools. CONTACT: [email protected] and [email protected]. SUPPLEMENTARY INFORMATION: A step-by-step tutorial is available in the Supplementary data at Bioinformatics online.

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ER -

GSATools: analysis of allosteric communication and functional local motions using a Structural Alphabet

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