Re: [ccp4bb] shape complementarity

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

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From: Krystle Williams McLaughlin krystle_w {- at -} HOTMAIL {- dot -} COM
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Subject: Re: shape complementarity
From: Francois Berenger berenger {- at -} RIKEN {- dot -} JP
Date: 2012-02-08

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

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
Division of Structural Biology
Walter and Eliza Hall Institute of Medical Research
1G Royal Parade, Parkville
Victoria 3052, AUSTRALIA

Tel. 61-3-9345-2693
Fax 61-3-9345-2686
Email: lawrence@wehi.edu.au

On 08/02/2012, at 12:08 PM, Francois Berenger wrote:

> 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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CCP4bb navigation

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

Previous message:
Subject: My hotmail address was hacked!
From: Krystle Williams McLaughlin krystle_w {- at -} HOTMAIL {- dot -} COM
Date: 2012-02-08

Next message:
Subject: Re: shape complementarity
From: Francois Berenger berenger {- at -} RIKEN {- dot -} JP
Date: 2012-02-08