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Author Topic: Calculating groove width- calladine algorithm  (Read 784 times)

Offline kailsen

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Calculating groove width- calladine algorithm
« on: April 30, 2012, 07:29:29 AM »
Hi ,
 I am interested to know the programming part of refined groove width calculation. I read this forum n found abt Calladine paper(1998). In their algorithm it says u fit a curve to three points. What formula was used (as there is more than one way of fitting a curve in 3D space) It will be nice tif u can explain how to go about considerding a example of say thre vectors, V1(x1,y1,z1) ; V2(x2,y2,z2) and V3(x3,y3,z3). Also it will be nice to know of any other algorithm/ work that talks about groove width calculation that is accepted  by Nucleic acid community. their advantages n disadvantages. esp with respected irregular deformed helices.

Offline xiangjun

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Re: Calculating groove width- calladine algorithm
« Reply #1 on: April 30, 2012, 11:00:44 AM »
As you know, 3DNA employs the El Hassan and Calladine algorithm to calculate major- and minor-groove widths. More specially, the appendix of the 1998 J. Mol. Biol. paper "Two Distinct Modes of Protein-induced Bending in DNA" was the sole reference based on which I implemented the groove-width algorithm. I am going to document the technical details, with an example, in the near future. However, if you really want to get to the bottom of the method, there is no substitute for reading carefully the original reference; after all, the appendix is only less than three pages long.

Quote
Also it will be nice to know of any other algorithm/ work that talks about groove width calculation that is accepted  by Nucleic acid community. their advantages n disadvantages. esp with respected irregular deformed helices.
This is not a light topic, which certainly cannot be fully addressed in a forum post, at least in my understanding. However, I assume that you are (or should be) aware of Curves/Curves+ which "provides a full analysis of groove widths and depths".

Given your deep interest in groove calculation, have you surveyed the literature? Do you know of other references than those two mentioned above? It would be helpful if you could share such information with us -- I'll consider to add the groove depth parameter if it fits in with 3DNA.

Xiang-Jun
« Last Edit: April 30, 2012, 02:12:54 PM by xiangjun »
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