Computational Chemistry Analysis

Jason Swails jason.swails at
Sun Feb 28 22:58:44 EST 2016

On Wed, Feb 24, 2016 at 8:01 PM, Feagans, Mandy <af154 at>

> Dear Python,
> Hi! I am a student interested in conducting computational analysis of
> protein-ligand binding for drug development analysis. Recently, I read of
> an individual using a python program for their studies of protein-ligand
> binding. As I have been reading about Python programs, however, all I have
> been able to find are programs that use the python script (i.e. Autodock).
> I was hoping to see if there were any programs specifically run through the
> python programming that ran similar analysis to Autodock?

​Being trained as a computational chemist myself (and having learned Python
by writing a program for carrying out protein-ligand free energy
calculations:, I had to

There are a number of programs out there that are aimed at computational
modeling of biomolecules, and many of them are written in Python or have
Python interfaces (pymol, chimera,, OpenMM to name a very small
few).  However, this is definitely not the right forum to ask such
questions as a very small number of people who frequent this list are
computational chemists (I check it only occasionally).

Looking for a program to do something because it's written in Python is the
wrong way to go about this.  You need to design your experiment (i.e., what
you want to test and what you hope to learn), then try to design a set of
calculations and analyses that will allow you to probe your underlying
hypothesis.  Then you should pick the software to perform these analyses
based on the best choice.  That choice is very frequently whatever others
in your lab are using.  A research group builds up experience (based
originally on the experience of the PI, typically) in a set of programs
they use for their computational experiments, and deviating from that set
of programs essentially discards potentially decades worth of experience.
So my suggestion -- ask other group members or the professor what softwares
they use, and consult Google if you wish to branch out a little.

You can also find more applicable mailing lists to ask questions about
computational chemistry, like the CCL or molecular dynamics news (the CCL
being the defacto "Computational Chemistry List").  That should help give
perhaps more helpful places to start.

FWIW, I did all my work with the AMBER and OpenMM software suites, (and
wrote a substantial amount of code for both projects).  But those are far
from the only options out there.


Jason M. Swails
Rutgers University
Postdoctoral Researcher

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