Re: [ccp4bb] shape complementarity calculations

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

CCP4bb navigation

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

Previous message:
Subject: Re: elbow and compound library
From: Judith Murray-Rust judith {- dot -} murray-rust {- at -} CANCER {- dot -} ORG {- dot -} UK
Date: 2009-03-03

Next message:
Subject: Re: shape complementarity calculations - oops!
From: "Edward A {- dot -} Berry" BerryE {- at -} UPSTATE {- dot -} EDU
Date: 2009-03-03

Subject: Re: shape complementarity calculations
From: "Edward A {- dot -} Berry" BerryE {- at -} UPSTATE {- dot -} EDU
Date: 2009-03-03

Actually sc is part of the ccp4 package.
(more $CDOC/sc.doc)
The reference describing the procedure is:
1. Michael C. Lawrence and Peter M. Colman J. Mol. Biol., 234, p946 -
p950 (1993)

As you say, it calculates shape complimentarity of the surfaces as they
are docked in the structure. So before you attribute changes in sc to
conformational changes, be sure the surfaces haven't moved wrt each other!

Cheers,
Ed

Oganesyan, Vaheh wrote:
> Colleagues,
>
> Would some one kindly suggest software that calculates shape
> complementarity of two interacting proteins based on co-crystal
> structure?
> I've seen number of reports with "sc" parameter included but none of
> those mention how it was done.
> Among non-runnable programs in CCP4 there is the sc program that indeed
> does not run.
>
> Thanks in advance.
>
> _______
> Vaheh
>
>
>
>
> To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation.
>

CCP4bb navigation

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

Previous message:
Subject: Re: elbow and compound library
From: Judith Murray-Rust judith {- dot -} murray-rust {- at -} CANCER {- dot -} ORG {- dot -} UK
Date: 2009-03-03

Next message:
Subject: Re: shape complementarity calculations - oops!
From: "Edward A {- dot -} Berry" BerryE {- at -} UPSTATE {- dot -} EDU
Date: 2009-03-03