Re: [ccp4bb] Binding pocket volume

Protein crystallography Programs for crystallography X-ray detectors
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CCP4bb <-- 2007 <-- April 2007 <-- 11 April 2007

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Subject: Re: AW: antibody refinement in REFMAC with Kabat numbering
From: Klaas Decanniere kdecanni {- at -} VUB {- dot -} AC {- dot -} BE
Date: 2007-04-11

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From: Ulrich Genick genick {- at -} BRANDEIS {- dot -} EDU
Date: 2007-04-11

Subject: Re: Binding pocket volume
From: artis {- at -} CHEMISTRY {- dot -} MONTANA {- dot -} EDU artis {- at -} CHEMISTRY {- dot -} MONTANA {- dot -} EDU
Date: 2007-04-11

Hello Yingjie Peng
You can do this in SPOCK. You can select all the residues that make up the
pocket and select calculate, volume from the menu for these residues. Hope
this works.
Arti

> Dear all,
>
> Is there anyone who can tell me how to calculate the volume of
> substrate
> binding pocket in a protein structure? I want to use it to the quantify
> the
> conformational change caused by induced fitting. Thanks very much.
>
> Yingjie Peng
>
> Yingjie PENG, Ph.D. student
> Structural Biology Group
> Shanghai Institute of Biochemistry and Cell Biology (SIBCB)
> Shanghai Institute of Biological Sciences (SIBS)
> Chinese Academy of Sciences (CAS)
> 320 Yue Yang Road, Shanghai 200031
> P. R. China
> 86-21-54921217
> Email: yjpeng@sibs.ac.cn
>

Arti S. Pandey
Graduate Student
Chemistry and Biochemistry
Montana State University
Bozeman,MT 59717

CCP4bb navigation

CCP4bb <-- 2007 <-- April 2007 <-- 11 April 2007

Previous message:
Subject: Re: AW: antibody refinement in REFMAC with Kabat numbering
From: Klaas Decanniere kdecanni {- at -} VUB {- dot -} AC {- dot -} BE
Date: 2007-04-11

Next message:
Subject: esu of coordinates DPI formula
From: Ulrich Genick genick {- at -} BRANDEIS {- dot -} EDU
Date: 2007-04-11