Some details on PNAS98 DNA sequence-dependent deformability

[xiangjun]

Recently I received a request from Mauricio, a graduate student from Dr. Olson's laboratory, for a technical question on generating the potential energy contour plots in the Olson et al. 1998 PNAS paper [PNAS98], "DNA sequence-dependent deformability deduced from protein–DNA crystal complexes." Then I vaguely remembered another PNAS98-related request from Dr. Olson several years ago, regarding details of data processing procedures.

PNAS98 is published a dozen years ago, and over the years it has made a big impact on the area of DNA-protein interactions, as evident by its over 400 citations. In retrospect, I was involved in the project mostly from a "technical" perspective: Andrey Gorin collected and analyzed (using CompDNA) the original DNA-protein complexes, and left the Olson lab before I came. I took over the project and performed further processing to generate all the table and figures used in PNAS98.

After publishing PNAS98, I have never done any follow up work regarding energetics of DNA-protein interactions. So all PNAS98-related files and scripts had been sleeping around, until I was contact by Dr. Olson in early 2006. It took me quite a while to dig them out, cleaned up and put them together. Four years later, now when Mauricio asks me a related question again, I tried to trace the emails I communicated with Dr. Olson on this matter. Unfortunately, my rutchem email account ceased to function from around summer 2006. So I have to check  backups from old machines I used ages ago ... It is from this time-consuming process (again) that I've decided to write this post to put together all PNAS98-related information I have collected, for the benefit of easy future reference.

The tarball PNAS98_Data.tar.gz contains the raw data I received from Gorin, and the scripts I used for further processing. See the included README.pdf and index.html for details. The Matlab script Ro_Tw_WKO.m was used to generate the ellipsoids contour plots of potential energies.  Around 1998, I think the version of Matlab I used was 5.x. Note that I do not have access to Matlab on my desktop nowadays.

For reasons detailed above, if you have further questions regarding PNAS98, please post them here instead of sending me emails, and I will try my best to answer them.

Xiang-Jun

[mauricio esguerra]

Dear Dr. Lu,

Thanks a lot for taking the time to dig into your old records and putting this together.
I have done my data processing using R instead of matlab, which is nice to use since it has a very active community of developers constantly adding a lot of functionality and graphic "eye-candy". As soon as I sort out the details that I was having trouble with on reproducing your results from your PNAS98 paper I will follow your example and post a tar.gz file here with the R code.

Thanks once more,

Mauricio