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Today's Topics:

  1. Re: Is it possible to calculate energy for the given
      structure with MODELLER's C API and derivative with respect to
      all coordinates (x, y, z)? (Modeller Caretaker)
  2. Re: homology modelling with multiple subunits (Modeller Caretaker)
  3. Regarding protein 3D structure modeling (vishal Nemaysh)
  4. Re: Regarding protein 3D structure modeling (Modeller Caretaker)


----------------------------------------------------------------------

Message: 1
Date: Thu, 22 Mar 2012 13:44:59 -0700
From: Modeller Caretaker <modeller-care@salilab.org>
To: Valerio Lupperger <valerio.lupperger@gmx.net>
Cc: modeller_usage@salilab.org
Subject: Re: [modeller_usage] Is it possible to calculate energy for
    the given structure with MODELLER's C API and derivative with respect
    to all coordinates (x, y, z)?
Message-ID: <4F6B8F4B.6020705@salilab.org>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

On 3/22/12 8:08 AM, Valerio Lupperger wrote:
> I use MODELLER (9.10) in a c-program like in
> http://salilab.org/modeller/manual/node456.html. As input I have one
> structure and its restraints. Is it possible to calculate energy for the
> given structure with MODELLER's C API and derivative with respect to all
> coordinates (x,y,z)? And if so, how is it possible?

If you can do it in a Python script, you can generally do it with the C
API (most of the Python interface to Modeller is simply calling the C
API underneath, in the _modeller module). So you can write the
equivalent Python code, and then look at Modeller's Python interface to
see what the equivalent C API functions are that it's calling. For
example, to calculate the energy you would call the energy() method in
the selection class; if you look at modlib/modeller/selection.py you'll
see that that method calls the C API mod_energy() function. In C you
will have to manually keep track of memory and handle errors, of course,
which is done automatically for you by the Python interface.

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


------------------------------

Message: 2
Date: Thu, 22 Mar 2012 13:48:48 -0700
From: Modeller Caretaker <modeller-care@salilab.org>
To: "Zumot, Elia Nabil" <enz1@pitt.edu>
Cc: "modeller_usage@salilab.org" <modeller_usage@salilab.org>
Subject: Re: [modeller_usage] homology modelling with multiple
    subunits
Message-ID: <4F6B9030.60402@salilab.org>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

On 3/22/12 10:53 AM, Zumot, Elia Nabil wrote:
> Is there a way to generate a homology model using several subunits as
> template? The protein I wish to model is a homotrimer. Am I wrong or
> is what is explained in "Building a model from multiple templates"
> not relevant here since I need the three subunits together in space
> (without steric clashes).

Unless I don't understand your question, this is covered by
http://salilab.org/modeller/9.10/manual/node28.html

Modeller is not going to magically determine the interface region
between your subunits and dock them, of course. You need to give it
information about the interface between subunits (either by giving it a
multimeric template, or by supplying it with subunit-subunit restraints
if you only have monomeric templates).

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


------------------------------

Message: 3
Date: Sat, 24 Mar 2012 11:27:49 +0530
From: vishal Nemaysh <vishal.bioinfotech@gmail.com>
To: modeller_usage@salilab.org
Subject: [modeller_usage] Regarding protein 3D structure modeling
Message-ID:
    <CALCM-RALrVh0c_NhOOVBKU_XvMQiFnnkyi-=18+1qHgasQWrJQ@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Hello Sir or all group members,

i have an amino acid sequence and the length is (1106 amino acid). so plz
tell me how can i model the complete 3D structure of this much lengthy
sequence.

thanking you,

Your Sincerely

--
Vishal
Research Scholar,
University of Delhi,
North Campus
Delhi-110007
M: 91+9650736653
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Message: 4
Date: Sat, 24 Mar 2012 09:57:30 -0700
From: Modeller Caretaker <modeller-care@salilab.org>
To: vishal Nemaysh <vishal.bioinfotech@gmail.com>
Cc: modeller_usage@salilab.org
Subject: Re: [modeller_usage] Regarding protein 3D structure modeling
Message-ID: <4F6DFCFA.4000901@salilab.org>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

On 3/23/12 10:57 PM, vishal Nemaysh wrote:
> i have an amino acid sequence and the length is (1106 amino acid). so
> plz tell me how can i model the complete 3D structure of this much
> lengthy sequence.

Modeller has no maximum length; modeling a large protein is exactly the
same as modeling a small protein. You might have to tweak
automodel.max_ca_ca_distance if the protein is especially large though:
http://salilab.org/archives/modeller_usage/2011/msg00268.html

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


------------------------------

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End of modeller_usage Digest, Vol 11, Issue 34
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