In general the transfer of ligand with remaning flexibility shoud imitaqte such induced fit, right?
Best regards,
Andrew
21.10.2011, 14:40, :
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> 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 <>
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> 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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> 1. Re: Modeling GPCRs (Modeller Caretaker)
> 2. Re: Modeling GPCRs (Hugo Gutierrez de Teran)
>
> ----------------------------------------------------------------------
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> 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: <>
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> 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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