[AMBER-Developers] Accuracy of the LCPO approximation

From: David A Case <case.biomaps.rutgers.edu>
Date: Thu, 17 Nov 2011 13:26:51 -0500

On Tue, Oct 04, 2011, Scott Le Grand wrote:

> As someone who wrote a *really* fast SASA approximation 18 years ago
> (basically Shrake and Rupley on steroids), here's my two cents.
> The Still et al. approximation at the heart of GBSA has a correlation
> coefficient of ~0.3 with the actual SASA. On the bright side, this
> approximation has a derivative.
> So if you're happy with some indeterminate analytic function of the number
> of atoms surrounding a given atom as a surrogate for accurately calculating
> the SASA, carry on... I'm not.

I'm moving this from the amber list to the amber-developers list. What Scott
said didn't agree with what I remembered from a decade ago, so I asked Dan
to look into this question, and his initial results are attached.

Basically, although there are some real limitations with LCPO, a
description of it as an "indterminate analytic function" with low
correlation to the actual SASA isn't correct for this particular test.
Correlation coefficients of 0.86 and 0.99 are found in the two cases looked at

So: finding out more about what types of tests lead to the bad results would
be useful, and it would also be nice to know about other approximations that
we should consider.


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Received on Thu Nov 17 2011 - 10:30:07 PST
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