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Author Topic: RAS Oncogenes In Three Dimensions?  (Read 2484 times)

Offline AlanWhite

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RAS Oncogenes In Three Dimensions?
« on: November 25, 2016, 02:59:10 pm »
I can find nucleotide base pair sequences for all the variants of the RAS Oncogene on the COSMIC Tumor Database website. What I can't find is three dimensional images of the RAS Oncogenes based on their separate and distinct nucleotide base pair sequences.

Is there a website where I might copy and paste a RAS gene base pair sequence into a window and be rewarded with a three dimensional image of the gene?   

Offline xiangjun

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Re: RAS Oncogenes In Three Dimensions?
« Reply #1 on: November 25, 2016, 03:36:52 pm »
As you may already know, the Protein Data Bank (PDB) holds experimentally determined 3D structures of macromolecules, including DNA, RNA, and their complexes with proteins and small molecules. Other than that, there exist computataional tools to predict 3D RNA structures from given base sequence, see RNA Puzzles. However, it is up to the users to decide whether a specific prediction is meaningful.

It is worth noting that, by and large, 3DNA does not predict 3D structures from 1D sequences. It does the opposite: by starting from a 3D model, 3DNA calculates a set of geometrical parameters to characterize the structure.

Xiang-Jun
« Last Edit: November 25, 2016, 09:49:16 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline AlanWhite

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Re: RAS Oncogenes In Three Dimensions?
« Reply #2 on: November 25, 2016, 04:37:39 pm »
I tried the Protein Data Bank. Their images are derived for genes in oddball organisms and under strange circumstances. I want to image the Ras oncogenes one at a time. Make changes in base pair composition and then compare the images (pre-malignant - post-malignant) against one another. Do you have an opinion about the software at this website:
http://bioinf.uni-greifswald.de/augustus/

Offline xiangjun

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Re: RAS Oncogenes In Three Dimensions?
« Reply #3 on: November 25, 2016, 05:28:46 pm »
The link your referred to says "AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences." Your question is on predicting RAS oncogenes in 3D. There seems a gap in between, as far as I can tell. You may want to ask the maintainer of the Augustus software for clarification.

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline AlanWhite

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Re: RAS Oncogenes In Three Dimensions?
« Reply #4 on: November 25, 2016, 09:17:41 pm »
Thanks for your comments. I just downloaded and installed CHIMERA from the University of California in San Francisco. CHIMERA might be the answer to my questions and the solution to my problems. And it's Freeware!

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.