Institute of Chemistry - University of Campinas

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1. Description of MDLovoFit capabilites and expected results.
    Read this to understand what to get from the package.
2. Step by step tutorial on how to use the package in your simulation.
    Follow the tutorial and get the results from your simulation.

1. Description of MDLovoFit capabilites and expected results.

First, we will show which information is expected from the usage of this package. Two plots are characteristic of the analysis of the data performed by MDLovoFit. Figure 1 illustrates the analysis of the mobility of a protein structure in a typical MD simulation:

Figure 1

The panel A of Figure 1 shows the standard RMSD of the protein Cα atoms along the simulation. It indicates that the protein somewhat diverges from the initial structure.

Figure 1B is the result of running MDLovoFit with the -mapfrac option. It shows the RMSD of the alignment of a subset of the atoms, as a function of the size of this subset, represented as a fraction of the size of the structure. For each fraction the RMSD is the best possible RMSD that can be obtained for every possible subset of that size. The plot shows, for example, that it is possible in this simulation to align about 80% of the Cα atoms of the structure to less than 1Å

Finally, in figure 1C, the RMSD computed by MDLovoFit for the alignment of 70% of the Cα atoms is shown. Clearly, the fluctuations of 70% of the structure are minimal, while there is a small subset of of 30% of the atoms that deviates from the initial structure and explains the divergence observed in figure 1A.

The result of figure 1C can, of course, be supported by the visualization of the resulting alignment. The structural alignment is shown in Figure 2. This figure can also be obtained from the output of MDLovoFit (and using VMD)

Figure 2

This figure displays, in blue, the 70% of the Cα atoms of the protein which were automatically identified by MDLovoFit as the least mobile ones (with RMSD lower than 1Å, as shown in figure 1C). In red, the figure highlights which regions of the structure are more mobile, and diverge from the initial conformation of the simulation.

With the plots of figures 1B and 1C, and with the above structural representation, a more comprehensive view of the mobility of the protein is obtained. In the next section we will show how to, in practice, obtain each of these plots.

Additionally, it is possible to plot the RMSF of the atoms, and to use these data to color the structure, using VMD. See the last section of the tutorial (next section) for details.
See also:
Author's software page
The TANGO project