Having run a molecular dynamics simulation,
extracting the answers to your questions from the
trajectory is the final step to a successful research
project. Unfortunately MD trajectory analysis is often a
big hurdle, since there are infinitely many things to
investigate, and pre-built software can often not do
exactly what you are looking for.
YASARA offers a very different approach,
which gives you the freedom to design your own analysis
with minimal efforts, building on a large number of
existing analyses and examples.
YASARA will not just create a text file
with results, but instead write a detailed
scientific report about the analysis for you,
with plots and tables ready for publication. Look
at the automatically created report for an MD simulation
of the CCR5 chemokine receptor with bound Maraviroc,
which inhibits entry of HIV. The simulation of this
membrane protein has also been run automatically, using
file 4MBS and YASARA's
membrane protein simulation protocol.
The default analysis includes
the following tables, images and plots in the report:
- Composition of the simulated system: atoms, residues,
molecules, waters, ions.
- Automatic identification of the ligand (if present).
- Ray-traced images of the complete system, the solute
and the ligand.
- Size of the simulation cell to see how pressure
coupling influenced the simulation.
- Potential energy and energy components
- Surface areas of the solute: Van der Waals, molecular (Conolly) and solvent accessible surfaces.
- Overall protein secondary structure content
- Protein secondary structure per residue
- Number of hydrogen bonds within the solute and between
solute and solvent, helps to monitor protein folding
- List of hydrogen bonds made be the ligand.
- Per-residue number of contacts to identify structurally important core residues and loose regions.
- Per-residue contacts with the ligand (H-bonds, hydrophobic, ionic)
- Radius of gyration of the solute.
- Calpha, backbone and all-atom RMSDs of the solute with
respect to the starting- or another reference structure.
- Ligand movement RMSD (calculated after superposing the
receptor) and ligand internal conformation RMSD
(calculated after superposing the ligand).
- Calculation of the time-average solute structure.
- Identification of the minimum-energy solute structure.
- Calculation of Root Mean
(RMSFs), plotting the resulting per-residue B-factors of
- Calculation of the Dynamic Cross
(DCCM) and visualization not only of the matrix, but
also of the correlated motions directly in the protein
- Creation of high-resolution plots for direct inclusion
in scientific articles.
As mentioned above, there are infinitely
many things to analyze, so it is likely that your specific
question is not answered by the default report above.
YASARA makes it as easy as possible to add your own
analysis to the report. Often typing a single
line is enough to create the plot you need. For
example to analyze the distance between the HN5 hydrogen
of Maraviroc residue MRV and the OH atom of TYR 251, the
following line needs to be added to the analysis:
Plot "Distance HN5 Res MRV,OH Res TYR 251",
'Length of Maraviroc N5 hydrogen bond',
The example above measures the hydrogen bond length in each MD
snapshot, adds the measurements to the result table as a
new column named 'MrvTyrDis', and adds a plot named
'Length of Maraviroc N5 hydrogen bond' to the report,
with the Y-axis labeled 'H-bond length'.