Sunday, May 15, 2011

Posts in the 3DNA forum reach 600

As of May 6, the total number of posts in the 3DNA forum has reached 600. Created in March 2007, with my debut post titled "Welcome message from Xiang-Jun Lu", the forum is now over four years old. Overall, the forum has served its purpose pretty well. In answering questions, I've been increasingly referring to the posts in the forum. As a concrete example, see the thread of a recent question "Base pair step parameters with a missing base pair".

At less than three posts (about one question) per week on average, I've not felt too much stress in supporting the forum (and maintaining 3DNA) in my spare time. For the most part, I've enjoyed interacting with 3DNA users from everywhere in the world, and with diverse backgrounds. Following the Unix philosophy ("Write programs that do one thing and do it well. Write programs to work together."), 3DNA has proved to be robust and flexible in serving its ever-growing user community. As a matter of fact, few questions I received a couple of years ago were beyond my original consideration of the details while I wrote the code. It is this intimated knowledge of all the underlying algorithms and every bit of their implementations that allows me to answer users' questions quickly and concretely.

As time passes by, however, it has become evident to me that 3DNA needs to be further refined and extended to meet the ever changing needs of its user community. For example, over the past few months, several questions asked in the 3DNA forum are directly relevant but clearly beyond 3DNA's current capabilities. While I'd be interested in implementing some of the requested functionality that make sense to me, doing so is certainly over my spare time limit. On the other hand, my increased understanding of nucleic acid structures and accumulated software expertise make it simply an issue of time and effort to move 3DNA to the next level, far beyond its current application scope and impact.

With posts in the 3DNA forum reaching 600, and citations to 3DNA articles over 600 (Google scholar), I am hopeful something good will happen to the 3DNA project. After all, 6 is a lucky number in traditional Chinese culture.

Fifty years of operon

In the latest issue of Science, there is a one-page editorial titled "The Birth of the Operon" by François Jacob, who won the Nobel Prize in Physiology or Medicine in 1965:
What is the operon, whose 50th anniversary is being celebrated this week? The word heralded the discovery of how genes are turned on and off, and it launched the now-immense field of gene regulation. ... we cannot presume to know how new ideas will arise and where scientific research will lead.
In the next three paragraphs, Jacob provides an insightful and vivid description of his research related to the discovery of the "operon" – a structural gene-regulatory gene ensemble. In consonant with his comment on scientific discovery, he concludes:
Our breakthrough was the result of “night science”: a stumbling, wandering exploration of the natural world that relies on intuition as much as it does on the cold, orderly logic of “day science.” In today’s vastly expanded scientific enterprise, obsessed with impact factors and competition, we will need much more night science to unveil the many mysteries that remain about the workings of organisms.
It is worth noting that the Journal of Molecular Biology (JMB) has recently published a special issue [Volume 409, Issue 1, Pages 1-88 (27 May 2011)], titled "The Operon Model and its Impact on Modern Molecular Biology" with historical accounts and reviews to celebrate operon's 50th anniversary. It is because of this event that motivated me to read the Jacob and Monod 1961 JMB review article "Genetic regulatory mechanisms in the synthesis of proteins" – I have come across this paper so many times before, and should have definitely read it long ago!

Curves+ web server

Through Google Scholar, I become aware of the article online in Nucleic Acids Research (NAR), titled "CURVES+ web server for analyzing and visualizing the helical, backbone and groove parameters of nucleic acid structures" by Richard Lavery's group:
Curves+, a revised version of the Curves software for analyzing the conformation of nucleic acid structures, is now available as a web server. This version, which can be freely accessed at, allows the user to upload a nucleic acid structure file, choose the nucleotides to be analyzed and after optionally setting a number of input variables, view the numerical and graphic results online or download files containing a set of helical, backbone and groove parameters that fully describe the structure. PDB format files are also provided for offline visualization of the helical axis and groove geometry.
The website looks quite streamlined, with required input information all in a single page, and the test page also ran smoothly. In less than two years following the publication of Curves+, it is nice to see the Curves+ web server version available, making this analysis tool more readily available to the nucleic acids community.

Nowadays, it seems safe (to the best of my knowledge) to say that only 3DNA and Curves+ conform to the 1999 Tsukuba convention for the description of nucleic acid base-pair geometry, and each of them provides a web interface: web 3DNA and web Curves+.