Since plants are susceptible to biotic and abiotic attacking, they present short and long-term defense mechanisms that are mediated by several signaling molecules, such as salicylic acid (SA) [1]. However, the signal to distal plant regions is not driven by SA, but through methyl salicylate (MeSA) molecule. The MeSA is generated in a reaction catalyzed by SABP2 (catalytic site formed by Ser81, ...

In a recent study published in this journal, Winger et al. investigate the magnitude of the time step to integrate the equations of motion in simulations with the coarse-grained MARTINI force field, using an implementation of MARTINI in the GROMOS software. Based primarily on the drift in temperature and the magnitude of the energy fluctuations in bulk liquids, the authors conclude that a time ...

z The results published by Kandt, Schlitter, and Gerwert in a recent issue of Biophysical Journal (Kandt et al., 2004) on molecular dynamics (MD) simulations of bacteriorhodopsin (bR) trimer in a water/lipid environment represent a new and valuable step in the field of bacteriorhodopsin modeling and, more generally, in the developing field of simulations of fully integrated and functional membr...

Molecular simulation is an extremely useful, but computationally very expensive tool for studies of chemical and biomolecular systems. Here, we present a new implementation of our molecular simulation toolkit GROMACS which now both achieves extremely high performance on single processors from algorithmic optimizations and hand-coded routines and simultaneously scales very well on parallel machi...

Background: Protein flexibility, which has been referred as a dynamic behavior has various roles in proteins’ functions. Furthermore, for some developed tools in bioinformatics, such as protein-protein docking software, considering the protein flexibility, causes a higher degree of accuracy. Through undertaking the present work, we have accomplished the quantification plus analysis of the varia...