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Author Topic: deformation energy calculation program  (Read 3919 times)

Offline tgaillar

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deformation energy calculation program
« on: December 15, 2008, 03:01:29 pm »
Hello,

I have written a program in C to calculate deformation energy scores on DNA duplexes from 3DNA output, based on X-ray averages and force constants at the base-pair or base-pair step level. This program gives not only the total deformation energy but also its components. I attach an archive containing the program as well as 3DNA output files to perform two tests:

deform_energy.tar.gz

- deformation energy of DNA in the 1kx5 nucleosome structure:
./deform_energy dna_1kx5.out

-> this test is able to reproduce the results of Tolstorukov et al. (2007), J. Mol. Biol. 371, 725-738, Table 1.

- deformation energy of two identical duplexes with inverse order of strands in the PDB file:
./deform_energy gact.out
./deform_energy gact-inv.out

-> the same total deformation energy is obtained for the two duplexes as expected!

Please note that these two tests fail with the deformation energy program currently distributed on the 3DNA website at:

http://rutchem.rutgers.edu/~xiangjun/3DNA/users.html  [see the post below -- Xiang-Jun Lu (Jan. 8, 2012)]

Dr. Thomas Gaillard
BioMaPS Institute
Rutgers University
610 Taylor Rd
Piscataway, NJ 08854
« Last Edit: January 08, 2012, 12:28:05 am by xiangjun »

Offline xiangjun

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Re: deformation energy calculation program
« Reply #1 on: January 07, 2012, 11:49:30 pm »
Quote
Please note that these two tests fail with the deformation energy program currently distributed on the 3DNA website at:

http://rutchem.rutgers.edu/~xiangjun/3DNA/users.html

The above note refers to the C++ program written by Marc Parisien (University of Montreal, Canada) for calculating deformation energies at the base-pair or dinucleotide step level. Since the referred to URL is now dysfunctional, I have consolidated all the related information here.

-- Xiang-Jun


Email message from Marc Parisien on the C++ program ('EnergyPDNA.C' and the associated header file 'EnergyParams.h' are attached below)

From parisien@iro.umontreal.ca
Date: Mon, 10 May 2004 11:28:18 -0400 (EDT)
From: Marc Parisien <parisien@iro.umontreal.ca>
Cc: xiangjun@rutchem.rutgers.edu, songliu@buffalo.edu
Subject: DNA deformation energy!


Hi All!

   I have received the mean values from Dr. Lankas;

        Lankas F, Sponer J, Langowski J, Cheatham TE 3rd.
          DNA deformability at the base pair level.
          J Am Chem Soc. 2004 Apr 7;126(13):4124-5.

   We now have the base-pair level deformation energies!!
   I have updated the program; see attached files :-)


   I have decoupled the energy calcs since there is the possibility
of coupled interactions between base-pairs and base-steps parameters...
(like Propeller-Rise, etc)   another article maybe for that ;-)
It would generate a huge matrix though: 12 x 12  (6 params for bases + 6
params for steps = 12 total params).

   I have also change the energy calcs loops from:

   1)
   i = 0 to 5  // the 6 parameters
   j = 0 to 5

   to

   2)
   i = 0 to 5
   j = i to 5

   because in 1) the i-j and j-i are counted twice, except for i-i,
   so it is not correct to then simply divide by 2.
   in 2) the i-j are counted singly, even for i-i.

   Regards,
   Marc.

//--------------------------------------------
Marc Parisien
parisien@iro.umontreal.ca
www-lbit.iro.umontreal.ca



Further note from Marc Parisien:

From parisien@iro.umontreal.ca Wed May 11 23:16:48 2005
Date: Tue, 19 Apr 2005 08:54:46 -0400 (EDT)
From: Marc Parisien <parisien@iro.umontreal.ca>
To: Bruno Contreras Moreira <contrera@ccg.unam.mx>
Cc: xiangjun@rutchem.rutgers.edu
Subject: Re: help with DNA deformation energy

Hi Dr. Bruno,


> I've just found your deformation energy code at
> http://rutchem.rutgers.edu/~xiangjun/3DNA
Cool!


> What's the energy reported? is it the energy that you need to apply to the
> system to obtain a given DNA deformation with a given sequence?
It is a deformation energy (units are kcal/mol, I think) based on
population preferences: E = -RT ln( P ) where P is the probability of
finding the sample in that conformation. This deformation energy reaches
back to Go where he analyzed the protein helix deformations (I don't
have that reference). I suggest that you imperatively read the 2 articles
mentionned in the "credits" section of the program (in the main()
routine).


> Do you need full-detail PDB coordinates of the DNA or the backbone is enough?
> Thanks for your feedback and for the code!!
Unfortunately, you need the full DNA since the energies come from the
side-chain conformations. You will have to launch the 3DNA program before
calculating the energies.


The energies reported here are not to be confused with those reported by
force-fields like AMBER or CHARMM... the energies here are those only from
population samples! You would have to do a thermodynamic cycle to obtain
the energy to apply to the system to obtain a given DNA deformation with a
given sequence!


As an application of this program you can look at a DNA/Protein complex
and do in-silico DNA mutations by changing the nature of the nucleotides
but without modifying the DNA 3D structure... You can then select the best
DNA sequence for that particular DNA 3D structure...


Do not mix the 2 energies calculations: use my program with the "-s"
option (the step energy) or with "-b" (the base-pairs energy)...



    Regards,
      Marc.

//--------------------------------------------
Marc Parisien
parisien@iro.umontreal.ca
www-lbit.iro.umontreal.ca


« Last Edit: January 08, 2012, 12:14:16 am by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.