My software notes

March 14, 2007

predict random coil relaxation (R2) values

Filed under: softwares and scripts — kpwu @ 6:24 pm

Recently, I’ve made a shell script that can generate a gaussian distribution-like random coil relaxation R2 values. The result is shown in the following figure. The script is kind of dirty hack, so I won’t paste the code at here. I’ll post it later when I have time to organize the code and make it more user-friendly.

Reference:

  1.  Protein Sci. 2006 Jun;15(6):1397-407.
  2. J Biomol NMR. 2006 Jul;35(3):175-86.
  3. Science. 2002 Mar 1;295(5560):1719-22.
  4. Biochemistry. 1997 Jul 22;36(29):8977-91. (Original paper)

rc-r21.png

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2 Comments »

  1. […] Here are two examples plots I made by Matlab after practicing few hours to know the language. Top plot is the Karplus equation for JHNHA scalar coupling constant and the bottom one is a theoretical R2 values of a fully random-coil like 140-aa protein (see my old post). […]

    Pingback by learning matlab « My software notes — October 12, 2007 @ 8:04 am | Reply

  2. This is Dinesh from TIFR, Mumbai.
    I have done R1, R2 and NOE experiments in denatured state of a protein on 800 MHz field. In order to take some idea about chemical exchange contribution i need the script for calculating “theoretical random-coil R2 values for my sequence”.
    Will you please forward the script.

    Comment by Dinesh Kumar — April 25, 2008 @ 11:26 am | Reply


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