ADL: Vina Question

Oleg Trott trott at scripps.edu
Wed Feb 12 11:16:45 PST 2014


On Mon, Feb 10, 2014 at 9:32 PM, Arjun Subramaniam
<arjunsubway at gmail.com> wrote:
> Hello,
>
> I am a high school student who is conducting biological research at
> Stanford, and I am hoping to use computer simulations to augment the
> biological work. Thanks for creating such a great software - It really is
> remarkable.
>
> One question - How do we analyze the results? I seem to be given a list of
> modes and the binding affinities and rmsd values of each mode, but I don't
> quite know what they mean. Are negative binding affinities like -10
> indicative of better or worse ligand-receptor binding than values like -4,
> or is it specific to each situation? And if it is specific to each
> situation, how do we figure out how good the binding affinity is?

http://en.wikipedia.org/wiki/Binding_constant

Vina tries to predict "delta G" in kcal/mol. Lower (more negative)
values are better binders.

-- 
Oleg Trott, Ph.D. (Columbia University)

Staff Scientist in the Olson Lab
The Scripps Research Institute

http://olegtrott.com


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