Characterizing the shape, motions, transitions, and interactions of
molecules that perform biological functions is an open
challenge in the field of structural biology. While wet lab
techniques (such as X-ray crystallography, nuclear magnetic resonance (NMR),
and cryo-EM) continue to provide valuable insight into the structure
that proteins assume to perform their biological function, these processes
have limitations. First, the environment in which the protein(s) are
measured/observed are, in some cases, very different than the
environment where they perform their function. Second, some behaviors,
such as the initial folding process or a structural rearrangement
after interacting with other molecular partners, are not adequately
captured by these techniques. Thus, computational methods
are needed to expand the observations and data collected from the
wet lab and allow us to postulate and model these bioactive molecules
so that we can better understand the mechanisms that are employed
to allow them to carry out their function.
In our lab, proteins are visualized using PyMol.
Both an academic/non-profit version (discounted) and a
free student version are
avilable. For work in this lab, we recommend you download the
free student version.
Note: that is you are using a VM, PyMol utilizes OpenGL for rendering,
and as a result, does not peform well in these environments.
The main software packages that will be installed include: