MDLovoFit

Institute of Chemistry - University of Campinas

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MDLovoFit is a package for the analysis of the mobility and structural fluctuation in Molecular Dynamics simulations. It allows the automatic identification of rigid and mobile regions of protein structures.

For example, it is possible to automatically identifiy a stable region of a protein in simulation in which the protein displays high structural flexibility, as illustrated in the figure on the right. The regions of low mobility are automatically detected by the method.

The software provides, as output, the Root-Mean-Square Deviations of the conserved structures, and of the divergent structures. A trajectory PDB file is output for the visualization of the results.

This software is distributed as FREE software, under the terms of the General Public Licence. Please cite the following reference if it was useful:
   L. Martínez, Automatic identification of mobile and rigid substructures in molecular dynamics simulations and fractional structural fluctuation analysis. PLoS One 10(3): e0119264, 2015. [LINK]
If you have any problem, comment or suggestion regarding this package, please contact Leandro Martínez at leandro@iqm.unicamp.br. Please report bugs!

Identification of a conserved core in the Thyroid Hormone Receptor ligand binding domain in a simulation of protein denaturation.
See also:
Packmol
LovoAlign
LovoFit
M3G home-page
The TANGO project