Re: [ccp4bb] 3D structure based alignment

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From: John R Helliwell jrhelliwell {- at -} GMAIL {- dot -} COM
Date: 2008-03-28

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Subject: Re: 3D structure based alignment
From: hua jing jing_hua {- at -} HOTMAIL {- dot -} COM
Date: 2008-03-28

Hi Tania,

A classical way of superimposing two structures is to use lsq_e and lsq_i commands in O . You can specify the regions that you want to match and visualize the superimposed structures right away to see if they make sense or not. O will also give you a pairwise sequence alignment and RMSD for the matched Ca atoms. You can superimpose more structures to the reference structure, if necessary, and save all the results in one file for visualization later. A new standalone Mac OS X version was just released two weeks ago (http://xray.bmc.uu.se/markh/ostick.html).

There are also a number of other programs available now for structure-based alignments. See the discussions on CCP4BB a few weeks ago. One program that was not mentioned is STAMP (http://www.compbio.dundee.ac.uk/Software/Stamp/stamp.html). It can produce high quality multiple sequence alignments, identify the most representative structure, and perform thorough statistical analysis (if I remember right).

HTH.

Holly
________________________________
> Date: Fri, 28 Mar 2008 17:20:39 +0000
> From: taniao@ITQB.UNL.PT
> Subject: [ccp4bb] 3D structure based alignment
> To: CCP4BB@JISCMAIL.AC.UK
>
>
> Hello,
>
> I´m having a problem that I would like to know if someone could help me.
>
> I want to do a 3D structure based alignment of my protein with another one. The problem is that my protein has 2 domains, and the structure that I want to superimpose just have one. I can do the structure superimposition by hand, but I´m not being able to do the sequence alignment based on the 3D structure, because the program that I´m using (SSM) starts to superimpose the sequence of my second domain in the beginning of the sequence of my reference model (exactly the same thing that it does with the sequence of the first domain).
>
> Do you know if there is any program where I can do this.
>
> Thanks in advance,
>
>
>
>
>
> Tânia Oliveira, PhD Student
>
> Membrane Protein Crystallography and Microbial Biochemistry Laboratory - ITQB-UNL

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CCP4bb navigation

CCP4bb <-- 2008 <-- March 2008 <-- 28 March 2008

Previous message:
Subject: Microsymposium 9 at Osaka IUCr Congress
From: John R Helliwell jrhelliwell {- at -} GMAIL {- dot -} COM
Date: 2008-03-28

Next message:
Subject: Problem with the DLS instrument
From: Yingjie Peng yingjiepeng {- at -} GMAIL {- dot -} COM
Date: 2008-03-29