shape complementarity

From: Francois Berenger
Date: 8 February 2012 01:08


Hello,

After following the discussion on
"[ccp4bb] shape complementarity between protein and DNA surface",
is there someone here able to explain simply what the SC software
of CCP4 is calculating?

I mean, is there some intuitive/easy to understand explanation of what SC is calculating?

I know I should read the corresponding paper, but I'd like
someone to enlighten me before so I have better chances of understanding the article.

Thanks,
Francois.

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From: Mike Lawrence

Hi Francois

Here's a one-liner. The major concept behind the Sc coefficient is that it measures the extent to which, "on average", the normal vectors between closest-neighbour opposing points within the molecular interface are antiparallel.

Sc=1 implies that the surfaces fit exactly, all such vectors are perfectly antiparallel. Heuristically, Sc values of 0.86 are about as good as protein-protein interfaces get (see Nature. 2005 435, pp773-8). Values below 0.65 indicate relatively poor shape complementarity.

Use of a normal vector -based metric is considered superior to a distance-based metric, though Sc does have a distance-based weight applied to the normal dot products. Critical to this calculation is that the boundary of the buried molecular interface has to be discarded from the measure, as this region is intrinsically geometrically divergent. Sc is thus computed across only that part of the buried surface that might be expected to be shape complementarity, which makes it somewhat ill-suited to smaller interfaces.

All these details are in the JMB paper, which, unfortunately, there is no substitute for reading :-)

sincerely

Mike

Mike Lawrence, PhD

Associate Professor and WEHI Fellow

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From: Francois Berenger

Thanks a lot for this very nice answer.

I will definitely read your JMB article.

Best regards,
Francois.