Re: [ccp4bb] shape complementarity

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Re: shape complementarity
From: Mike Lawrence lawrence {- at -} WEHI {- dot -} EDU {- dot -} AU
Date: 2012-02-08

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From: "Edward A {- dot -} Berry" BerryE {- at -} UPSTATE {- dot -} EDU
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Subject: Re: shape complementarity
From: Francois Berenger berenger {- at -} RIKEN {- dot -} JP
Date: 2012-02-08

On 02/08/2012 12:47 PM, Mike Lawrence wrote:
> 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 :-)

Thanks a lot for this very nice answer.

I will definitely read your JMB article.

Best regards,
Francois.

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: shape complementarity
From: Mike Lawrence lawrence {- at -} WEHI {- dot -} EDU {- dot -} AU
Date: 2012-02-08

Next message:
Subject: Re: Freezing crystal
From: "Edward A {- dot -} Berry" BerryE {- at -} UPSTATE {- dot -} EDU
Date: 2012-02-08