Re: [ccp4bb] thread protein sequence using pdb coordinates that are not avaliable on RCSB?

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

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Subject: Re: thread protein sequence using pdb coordinates that are not avaliable on RCSB?
From: Robert Immormino immormino {- at -} GMAIL {- dot -} COM
Date: 2010-05-12

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Subject: Re: thread protein sequence using pdb coordinates that are not avaliable on RCSB?
From: Scott Pegan scott {- dot -} d {- dot -} pegan {- at -} GMAIL {- dot -} COM
Date: 2010-05-12

Kelly,

You can do it with swiss-model, just have to use the alignment mode. I will
ask for a pdb or RCSB code. Also, in the past I have found Jigsaw 3D model
server to be a comparable tool.

Scott

On Wed, May 12, 2010 at 10:10 AM, Kelly Daughtry wrote:

> Hello all,
> I would like to thread one protein sequence onto a structure I recently
> solved, and has not been submitted to the pdb.
>
> I found the swiss-model website, which is an excellent tool for inputing a
> template sequence and target sequence (which is what I want to do), but it
> only allows you to select a PDB ID, and not to upload your own pdb file.
>
> Does anyone know where I can do this online? I'm thisclose to just changing
> each amino acid in coot (with the amount of searching I've done, it's about
> equal time!).
>
> Thanks in advance,
> Kelly Daughtry
>
> *******************************************************
> Kelly Daughtry
> PhD Candidate
> Department of Physiology and Biophysics
> Boston University School of Medicine
> 590 Commonwealth Ave
> R 390
> Boston MA, 02215
> (P) 617-358-5548
> *******************************************************
>

--
Scott D. Pegan, Ph.D.
Assistant Professor
Chemistry & Biochemistry
University of Denver

CCP4bb navigation

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

Previous message:
Subject: Re: thread protein sequence using pdb coordinates that are not avaliable on RCSB?
From: Robert Immormino immormino {- at -} GMAIL {- dot -} COM
Date: 2010-05-12

Next message:
Subject: Positions to be filled in Lübeck?
From: mesters mesters {- at -} BIOCHEM {- dot -} UNI-LUEBECK {- dot -} DE
Date: 2010-05-12