Re: [ccp4bb] rigid flexible analysis

[van den Bedem, Henry]

KGS software can do this, as well as sampling based on rigidity 
(10.1016/j.jmps.2015.06.006<https://dx.doi.org/10.1016/j.jmps.2015.06.006> or 
10.1021/acs.jctc.5b00995). The software is available from github: 
https://github.com/ExcitedStates/KGS.

Henry

From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Gauri Misra 
<kamga...@gmail.com>
Reply-To: Gauri Misra <kamga...@gmail.com>
Date: Tuesday, January 24, 2017 at 3:46 AM
To: "CCP4BB@JISCMAIL.AC.UK" <CCP4BB@JISCMAIL.AC.UK>
Subject: [ccp4bb] rigid flexible analysis

Hi everyone!

I would like to know the current online servers available for analyzing the 
rigid and flexible regions of proteins.Looking forward for precious inputs from 
the community.

Sincerely,
Dr. Gauri Misra

Assistant Professor
Amity Institute of Biotechnology
Amity University
Noida (U.P.) India

Re: [ccp4bb] rigid flexible analysis

[Pavel Afonine]

Hi,

can't you infer this from refined atomic displacement parameters (ADPs;
also knowns as B-factors)?

Or run a 100 or so SA refinement jobs, each starting with a different
random seed. This will generate an ensemble of models with some atoms
occupying more conserved positions than the others.

Pavel

On Tue, Jan 24, 2017 at 3:46 AM, Gauri Misra  wrote:

> Hi everyone!
>
> I would like to know the current online servers available for analyzing
> the rigid and flexible regions of proteins.Looking forward for precious
> inputs from the community.
>
> Sincerely,
> Dr. Gauri Misra
>
> Assistant Professor
> Amity Institute of Biotechnology
> Amity University
> Noida (U.P.) India
>

[ccp4bb] rigid flexible analysis

[Gauri Misra]

Hi everyone!

I would like to know the current online servers available for analyzing the
rigid and flexible regions of proteins.Looking forward for precious inputs
from the community.

Sincerely,
Dr. Gauri Misra

Assistant Professor
Amity Institute of Biotechnology
Amity University
Noida (U.P.) India