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GSATools: analysis of allosteric communication and functional local motions using a structural alphabet.

Pandini A, Fornili A, Fraternali F, Kleinjung J - Bioinformatics (2013)

Bottom Line: 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; and (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.

View Article: PubMed Central - PubMed

Affiliation: Randall Division of Cell and Molecular Biophysics, King's College London, London, UK. alessandro.pandini@kcl.ac.uk

ABSTRACT

Motivation: GSATools is a free software package to analyze 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; and (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.

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Overview of the major analysis steps for the NtrC protein (Pandini et al., 2012). A high-resolution image is given in the Supplementary Data
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btt326-F1: Overview of the major analysis steps for the NtrC protein (Pandini et al., 2012). A high-resolution image is given in the Supplementary Data

Mentions: The g_sa_encode program provides two modes of encoding [local and global (Park and Levitt, 1995)] and yields several statistics metrics about the encoded trajectory. The user can visualize the time evolution of structural changes by a color-coded representation of the alignment (Fig. 1A). Additionally, the accuracy of the encoding can be measured and plotted for inspection. The extent of conformational variability at each position can be estimated by the Shannon entropy, and the relative frequency of the representative fragments at each position can be saved as a sequence profile of the alignment. Example graphs of these statistics are included in the Supplementary Data.Fig. 1.


GSATools: analysis of allosteric communication and functional local motions using a structural alphabet.

Pandini A, Fornili A, Fraternali F, Kleinjung J - Bioinformatics (2013)

Overview of the major analysis steps for the NtrC protein (Pandini et al., 2012). A high-resolution image is given in the Supplementary Data
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3722520&req=5

btt326-F1: Overview of the major analysis steps for the NtrC protein (Pandini et al., 2012). A high-resolution image is given in the Supplementary Data
Mentions: The g_sa_encode program provides two modes of encoding [local and global (Park and Levitt, 1995)] and yields several statistics metrics about the encoded trajectory. The user can visualize the time evolution of structural changes by a color-coded representation of the alignment (Fig. 1A). Additionally, the accuracy of the encoding can be measured and plotted for inspection. The extent of conformational variability at each position can be estimated by the Shannon entropy, and the relative frequency of the representative fragments at each position can be saved as a sequence profile of the alignment. Example graphs of these statistics are included in the Supplementary Data.Fig. 1.

Bottom Line: 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; and (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.

View Article: PubMed Central - PubMed

Affiliation: Randall Division of Cell and Molecular Biophysics, King's College London, London, UK. alessandro.pandini@kcl.ac.uk

ABSTRACT

Motivation: GSATools is a free software package to analyze 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; and (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.

Show MeSH