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Questions and answers => General discussions (Q&As) => Topic started by: sjo248 on March 18, 2015, 10:53:59 am

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Title: What is the difference between direct P-P measurement and refined
Post by: sjo248 on March 18, 2015, 10:53:59 am

I have searched and cannot find what the difference between the direct P-P measurement and the refined measurement when it comes to major/minor groove widths.  Can somebody please help?

Title: Re: What is the difference between direct P-P measurement and refined
Post by: xiangjun on March 18, 2015, 11:45:17 am

Here is an example output for the Dickerson dodecamer (355d), which contains the reference for groove widths 3DNA uses. Specifically, read the two-page appendix of the 1998 El Hassan and Calladine paper.

Code: [Select]

****************************************************************************
Minor and major groove widths: direct P-P distances and refined P-P distances
   which take into account the directions of the sugar-phosphate backbones

   (Subtract 5.8 Angstrom from the values to take account of the vdw radii
    of the phosphate groups, and for comparison with FreeHelix and Curves.)

Ref: M. A. El Hassan and C. R. Calladine (1998). ``Two Distinct Modes of
     Protein-induced Bending in DNA.'' J. Mol. Biol., v282, pp331-343.

                  Minor Groove        Major Groove
                 P-P     Refined     P-P     Refined
   1 CG/CG       ---       ---       ---       ---
   2 GC/GC       ---       ---       ---       ---
   3 CG/CG      14.3       ---      18.2       ---
   4 GA/TC      12.0      11.9      17.3      17.3
   5 AA/TT       9.7       9.6      19.1      19.0
   6 AT/AT       9.1       9.1      16.4      16.0
   7 TT/AA       9.1       9.1      17.8      17.7
   8 TC/GA       9.6       9.6      18.6      18.6
   9 CG/CG      10.4       ---      19.0       ---
  10 GC/GC       ---       ---       ---       ---
  11 CG/CG       ---       ---       ---       ---

HTH,

Xiang-Jun

Title: Re: What is the difference between direct P-P measurement and refined
Post by: sjo248 on March 18, 2015, 03:24:07 pm

I appreciate your response but I've already read that paper, and again reviewing the appendix didn't give me the answer.  I'm a grad student and new to this field, just doing a side project with a different P.I., but he didn't know the difference either.  I don't need calculations or anything, I just need to know how the two values differ.  I figured someone here would know since its reported in the 3DNA output.  Searching this website, or google didn't help me either.

Title: Re: What is the difference between direct P-P measurement and refined
Post by: xiangjun on March 18, 2015, 03:50:24 pm

The reference gives the definition of the two sets of groove widths. I implemented the algorithm reported in the paper after reading through the appendix many times.

Reading the original literature and examining sample 3DNA outputs should allow for a high-level understanding of two sets of groove widths. To really get to the bottom of the issue, I know of no better alternate than to implement the algorithm, which requires calculations and programming. I may misunderstand your question. Others on the Forum may be able to provide a more helpful answer.

You may want to try Curves+ which has a different way of calculating groove widths and depths.

Xiang-Jun

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University