MD Davis

A Python package to perform preliminary analysis of molecular dynamics trajectories. The source code can be found at:

What can MD Davis do?

  1. Create dynamic visualization of electric field around the molecule using PyMOL.
    Dynamics of electric field

  2. Create interactive plot for time series data: root mean squared deviation (RMSD) and radius of gyration

  1. Create Free energy landscapes using common ranges and number of bins.
  1. Create interactive plot of containing the following residue level properties:
    • root mean squared fluctuation (RMSF)
    • circular standard deviation of backbone dihedral angles
    • Secondary structure
    • Solvent accessible surface area
    • Mean and standard deviation for the total surface electrostatic potential per residue
    • Mean and standard deviation for the mean surface electrostatic potential per residue

It can also use an alignment to align the residue level data from different proteins along the x-axis. This ensures that the peaks line up properly for better interpretation.

Some instructions for creating these types of plots are available here: Instructions and instructions for calculating surface electrostatic potentials can be found here: Electrostatics

help for each command in MD Davis can be accessed with -h, for example

md_davis -h