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

Alessandro Pandini | Zendy; Arianna Fornili | Zendy; Franca Fraternali | Zendy; Jens Kleinjung | Zendy

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

Author(s) -

Alessandro Pandini,

Arianna Fornili,

Franca Fraternali,

Jens Kleinjung

Publication year - 2013

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btt326

Subject(s) - allosteric regulation , computer science , software , alphabet , range (aeronautics) , r package , source code , identification (biology) , set (abstract data type) , license , algorithm , theoretical computer science , biological system , computational science , chemistry , programming language , biology , engineering , biochemistry , enzyme , linguistics , philosophy , aerospace engineering , operating system , botany

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.

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