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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. Augusto Pieroni Leggere La Fotografia Pdf File. 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. Contact: or Supplementary information: are available at Bioinformatics online.

1 INTRODUCTION Biomolecular motions play a key role in several biological functions: enzymatic activity, protein–protein interactions, ligand binding and allosteric regulation. Computational approaches, such as molecular dynamics (MD), are now routinely used to reproduce the intrinsic dynamics of proteins, but effective tools are still required to gain functional insight from the simulated data. Global collective motions are often associated with biological functions, and it was demonstrated that these motions can be extracted from conformational ensembles (). In a previous study, we suggested a method aimed at recovering the role of local conformational changes in functional motions (). To this purpose, we developed a structural alphabet (SA): a set of 25 canonical states of four-residue protein fragments (C α atoms only) describing the most probable local conformations in high-resolution protein structures. Therefore, the SA provides a means for the coarse-grained annotation and processing of local conformations in a string format, which lends itself to a range of efficient sequence analysis algorithms. Rapidshare World Paper Money more. The SA has been used successfully in analyzing local changes in implicit solvent simulations (), allosteric signal transmission () and conformational changes on effector binding ().