[modeller_usage] Oligomer Modelling

[Manjunatha Karpenahalli <>]

Dear Modeller users,

I try to model homedimer with few point mutations using hometrimer as a template. In the alignment file I specified to use only chain A and chain B from the template, but the out put dimer model has different monomer-monomer interface than template. I used standard script( http://salilab.org/modeller/9v4/manual/node28.html) and the alignment file:

>P1;inv3HD

sequence:inv3HD:1:.: 331 ::MODELLING PROTEIN:undefined::

MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQSLLIGVATSSLA

LHAPSQIVAAIKSRADQLGASVVVPMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVP

ALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTLNQIQPIAER

EGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAIAESGLRVGADISVVGYDDTEDSSCYIPPLTT

IKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLA\MKPVTLYDVAEYAGVSYQTVSRVVNQAS

HVSAKTREKVEAAMAELNYIPNRVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVPMVE

RSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVE

HLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTLNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLV

ANDQMALGAMRAIAESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGN

QLLPVSLVKRKTTLA*

>P1;1EFA

structureX:1EFA:2:A: 329 :.:LAC REPRESSOR:undefined::

-KPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQSLLIGVATSSLA

LHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKTAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVP

ALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAER

EGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTT

IKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLA*

>P1;1EFA

structureX:1EFA:2:B: 329 :.:LAC REPRESSOR:undefined::

-KPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQSLLIGVATSSLA

LHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKTAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVP

ALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAER

EGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTT

IKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLA*

Thank you very much in advance for any tips

-Manjunatha Karpenahalli

--- On Tue, 29/7/08, Modeller Caretaker <> wrote:

From: Modeller Caretaker <>
Subject: Re: [modeller_usage] Oligomer Modelling
To:
Cc:
Date: Tuesday, 29 July, 2008, 8:28 PM

Manjunatha Karpenahalli wrote:
> Is it possible to model home-tetramer using modeller?

Sure, see:
http://salilab.org/modeller/9v4/manual/node28.html

That example is for a dimer, but it is straightforward to use a similar 
script to model a tetramer.

	Ben Webb, Modeller Caretaker
-- 
             http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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