Secondary structure superimposition problem

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Vipul Yadav

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Sep 8, 2020, 10:13:02 AM9/8/20
to Phyre
Hi,
I have one wild type gene and one mutant gene having single mutation. They both have same sequence except for G260V change in mutant amino acid chain. I used Phre2 to make their secondary structure but when I used normal mode, the structure was incomplete and when I used intensive mode, the both structure were completely different and I was unable to superimpose both the structures.
Please help me with this.
Thanks

Tilahun Rabuma

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Sep 17, 2020, 3:25:47 AM9/17/20
to vipulya...@gmail.com, Phyre
You may ise swiftmodel 

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Sternberg, Michael J E

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Sep 17, 2020, 3:46:10 AM9/17/20
to tile...@gmail.com, vipulya...@gmail.com, Phyre

I am the PI of the Phyre team.

 

In the e-mail returning your results you will see Missense3D in addition to other tools that evaluates the impact of a missense variant.

 

 

===============================

=          NEW TOOLS

===============================

We are pleased to announce the following web-based resources to model the impact of missense variants on protein structures and to view protein structure

MISSENSE3D provides a stereochemical report (e.g. loss of an H-bond) on the effect of a missense variant on protein structure.

The approach has been designed (and benchmarked) to be effective on both PDB structure and predicted models, which will be less accurate.

A user can upload their own variant and coordinates.   (JMB in press https://www.sciencedirect.com/science/article/pii/S0022283619302037)

 

MISSENSE3D: http://www.sbg.bio.ic.ac.uk/missense3d/

 

 

PHYRERISK is a recently developed resource which maps genetic variants to experimental and predicted protein structures.

Our protein page currently clearly displays the experimental and predicted structures and shortly will include experimental and predicted binary complexes.  We use the VEP server at the EBI so, unlike several more protein centric resources, users can map from genetic coordinates. (JMB in press).

 

PHYRERISK: http://phyrerisk.bc.ic.ac.uk

 

EZMOL is an easy to use, web-based, wizard-drive, molecular graphics display.  It is designed for the occasional user who does not wish to invest the time to use programs such as PyMol and Chimera. Generated images can be downloaded for publication.

(See Reynolds, et al (2018). JMB)

 

EZMOL: http://www.sbg.bio.ic.ac.uk/ezmol/

 

 

 

 

********************************************

Professor Michael J E Sternberg

Director Centre for Integrative Systems Biology  and Bioinformatics  (CISBIO)  

Room 306 - Sir Ernst Chain Building

Department of Life Sciences

Imperial College London, London  SW7 2AZ,UK

m.ste...@imperial.ac.uk

http://www3.imperial.ac.uk/cisbio (CISBIO)

www.sbg.bio.imperial.ac.uk (Group's research)

 

Tel +44 (0)20 7594 5212

****************************************************************************

 

From: ph...@googlegroups.com <ph...@googlegroups.com> On Behalf Of Tilahun Rabuma
Sent: 14 September 2020 16:05
To: vipulya...@gmail.com
Cc: Phyre <ph...@googlegroups.com>
Subject: Re: [Phyre:176] Secondary structure superimposition problem

 

This email from tile...@gmail.com originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list to disable email stamping for this address.

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