MutInf
What is MutInf?
MutInf is an analysis package written in Python. inline C, and R that analyzes data from Molecular Dynamics
Simulations to identify statistically significant correlated motions and
calculate residue-by-residue conformational entropies. Our work has shown that
the pattern of mutual information between residues can be used to identify
couplings between allosteric sites and identify residues that might be important
in mediating these couplings.
Obtaining MutInf
MutInf is free for academic use. It will most likely be put
under tPlease contact Chris McClendon if you would
like a copy of the code.
If you use MutInf, please cite:
Christopher L. McClendon,
Gregory Friedland, David L. Mobley, Homeira Amirkhani, Matthew P.
Jacobson. Journal of Chemical Theory and Computation.
2009, 5 (9), pp 2486–2502.
The code works best with
Python 2.4.4 or 2.6.2, and requires NumPy and SciPy libraries, which take a bit of work to install but
are well-worth the effort. Alternatively, Schrodinger (http://www.schrodinger.com) bundles NumPy and SciPy with their
Maestro package, which is free for academics.
I recommend running MutInf on 64-bit machines with as much RAM is possible --
ideally 4GB-16GB.
One requirement of the method is that you have many thousands of trajectory
snapshots, ideally many tens of thousands. For six simulations of 10 ns each,
ideally you'd want to save snapshots every 0.5ps -- 1ps, though the method will
still work fine (but may reject some correlations as not statistically
significant) if you have snapshots every 10 ps,
though this is not recommended, unless your simulations are longer (i.e.
100ns). In Mike Gilson's papers that I cite, he keeps more snapshots than I do,
up to every 100fs. I use robust entropy estimators and statistical filters that
allow smaller sample sizes, so one can use thousands to tens if thousands of
snapshots instead of a million or more snapshots.
Acknowledgements
A very special thanks to Greg Friedland
for helping with code development and debugging. Without his help the code
would not be what it is today. Thanks also to Salma Rafi for being the first
end-user of the code and for using it in biologically-impactful applications,
and to Adam Steeves who is currently improving the
clustering/analysis protocol. Finally, thanks to my advisors, Matt Jacobson and
Jim Wells, for supporting and encouraging my study of allostery and the development
of this software.
Repository Access
MutInf's repository is on the SimTK site ( https://simtk.org/home/mutinf ), where a number of other useful simulation analysis tools can be found. Please contact
Chris McClendon (see Contact below) if you have any suggestions, bug reports,
patches, new features, etc.
MutInf Manual
1. Installation
2. Getting
dihedral angles from simulations
3. Specify residues
to analyze
4. Organize files
into MutInf’s official directory structure
5. Running
the program (and options)
6. Analyzing
the results (and output files)
8. Contact