Dear Modeller list administrators, I would like to change my subscription settings.
I want to get not digest but messages as soon as they are sent.
Sincerely yours,
Andrey
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21.10.2011, 14:40, :
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Today's Topics:
1. Re: modeller_usage Digest, Vol 10, Issue 123 (Ashish Runthala)
2. induced fit modeling by Modeller or ModLoop (Andrew Voronkov)
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Message: 1
Date: Wed, 19 Oct 2011 16:17:34 +0530 (IST)
From: Ashish Runthala <>
Subject: Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 123
To: modeller usage <>
Message-ID:
<>
Content-Type: text/plain; charset=utf-8
Sir Ben is correct. But there is an option to let your model be biased to its actual native state, instead of forcing it to the topology of your templates.
Select good templates which you might have already done correctly.
Now if you know how to make a correct representative alignment for your target, that is the best choice.
Or if you don't try to harness continuous or discontinuous reliable structural folds from templates as per your constraints.
Don't rely simply on MD to relax the models. If your first model is distant from its native state, no way you can pull it through. So focus on template selection and correct alignment to build your model through these reliable scaffolds.
Good Luck
Ashish
Ashish Runthala,
Lecturer, Structural Biology Cell,
Biological Sciences Group,
BITS, Pilani
Rajasthan, INDIA
----- Original Message -----
From: "modeller usage-request" <>
To: "modeller usage" <>
Sent: Wednesday, October 19, 2011 12:12:24 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi
Subject: modeller_usage Digest, Vol 10, Issue 123
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Today's Topics:
1. Re: Modeling GPCRs (Modeller Caretaker)
2. Re: Modeling GPCRs (Hugo Gutierrez de Teran)
----------------------------------------------------------------------
Message: 1
Date: Tue, 18 Oct 2011 17:52:46 -0700
From: Modeller Caretaker <>
Subject: Re: [modeller_usage] Modeling GPCRs
To: Maggie Pruitt <>
Cc:
Message-ID: <>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 10/18/11 1:57 PM, Maggie Pruitt wrote:
> I am interested in using Modeller for predicting the structure of the G
> protein-coupled receptor I study. This protein does not have any
> homologous proteins in the PDB database and there is no experimental
> data to help model the protein. Knowing this, can Modeller provide an
> accurate structure of my protein to use in molecular dynamics
> simulations? I understand that I can choose other crystallized GPCRs to
> use as templates, but I am concerned that since Modeller is a homology
> modeling program that the end model would simply look like my protein
> forced onto the template structure.
Yes, you are exactly correct. Modeller is not limited to using homologs
as templates; it can use any protein that you believe is structurally
similar to the protein you intend to model. But if you choose a template
that is not similar, you will likely get a poor model.
Ben Webb, Modeller Caretaker
--
http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
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Message: 2
Date: Wed, 19 Oct 2011 08:42:21 +0200
From: Hugo Gutierrez de Teran <>
Subject: Re: [modeller_usage] Modeling GPCRs
To:
Message-ID:
<CAG02diR1jQJizHkK4vM0RQm+>
Content-Type: text/plain; charset="iso-8859-1"
Maggie,
We have developed GPCRModSim, a web server that facilitates the process of
modeling GPCRs using Modeller as a back end modeling tool (
http://gpcr.usc.es).
In particular, once you upload your sequence or swissprot code, you will get
an optimized alignment with all crystallized GPCRs (you can choose also
between templates in the active or inactive conformations). The server will
recommend you the most suitable template based on TM homologies, although
you can further inspect this and change the default selection on the basis
of homologies between particular regions.
Please visit http://gpcr.usc.es
For a test case, the H1 histamine receptor modeled with excelent accuracy,
see the tutorial at http://gpcr.usc.es/tutorial
There are several other features, like the possibility of loop refinement
(using loopmodel routines) and the MD simulation of your simulated model in
an atomistic model of the membrane (using GROMACS routines).
Hugo
--
Hugo G. de Teran, PhD.
"Parga Pondal" Research fellow
Fundaci?n P?blica Galega de Medicina Xen?mica - SERGAS
Santiago de Compostela (SPAIN)
Phone +34 881813873
e-mail: http://webspersoais.usc.es/hugo.teran
2011/10/18 Maggie Pruitt <>
> Hello,
>
> I am interested in using Modeller for predicting the structure of the G
> protein-coupled receptor I study. This protein does not have any homologous
> proteins in the PDB database and there is no experimental data to help model
> the protein. Knowing this, can Modeller provide an accurate structure of my
> protein to use in molecular dynamics simulations? I understand that I can
> choose other crystallized GPCRs to use as templates, but I am concerned that
> since Modeller is a homology modeling program that the end model would
> simply look like my protein forced onto the template structure.****
>
> If anyone can give me some further insight on this manner, I would greatly
> appreciate it.
>
> Thanks in advance for your help!
>
> Sincerely,
>
> Maggie
>
> _______________________________________________
> modeller_usage mailing list
>
> https://salilab.org/mailman/listinfo/modeller_usage
>
>
--
--
Hugo G. de Teran, PhD.
"Parga Pondal" Research fellow
Fundaci?n P?blica Galega de Medicina Xen?mica - SERGAS
Santiago de Compostela (SPAIN)
Phone +34 881813873
e-mail: http://webspersoais.usc.es/hugo.teran
--
--
Hugo G. de Teran, PhD.
"Parga Pondal" Research fellow
Fundaci?n P?blica Galega de Medicina Xen?mica - SERGAS
Santiago de Compostela (SPAIN)
Phone +34 881813873
e-mail: http://webspersoais.usc.es/hugo.teran
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Message: 2
Date: Fri, 21 Oct 2011 14:40:28 +0400
From: Andrew Voronkov <>
Subject: [modeller_usage] induced fit modeling by Modeller or ModLoop
To:
Message-ID: <>
Content-Type: text/plain; charset=utf-8
Dear Modeller users, I need to model induced protein-ligand fit.
Flexibility is supposed to be defined mostly by only one of the loops in the protein, so I probably don?t need to do a molecular
dynamics, but can just make simulated annealing and conformational sampling for this loop.
Is it possible to do it somehow in parallel with protein docking ? for example with ligand present or by any other way
to include ligand influence on loop position?
But in general looks like the simplest way is to make loop sampling, perform docking and check final complexes by score/analyze manually.
Best regards,
Andrew
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