My software for RNA and DNA folding—secondary structure—prediction has been popular for many years and is widely used around the world. I have also offered this software in an easy-to-use format on the World Wide Web since 1996. It is called the "Mfold web server." The July '03 article is the first and only publication describing in detail what was already a popular web site. I ask people to cite this article if they publish articles containing useful results obtained on the Mfold web server.

The paper describes bioinformatics software that has been around and available for many years. The web site itself is quite "user friendly," with many hyper-links to help files and links to pages that define terms. The article does point out many features of the web site that were obscure and has probably thereby improved its effectiveness for many users.

It is perhaps ironic that I published this article when the server is stable and changing very little. It represents my past research. I plan a new web site in the very near future to make the fruits of my current research readily available to the scientific community.

The paper describes in detail a bioinformatics web server and what sort of computations can be performed on it. These kinds of calculations are useful to many scientists and educators. For example:

1. The server has been used by scientists to predict the folding and/or the binding of nucleic acid oligomers (short stretches of RNA or DNA) to "targets." Applications are to the design of nucleic acid probes that can be used for genotyping (which strain of Hepatitis C is in my sample?), PCR primer design, anti-sense drug design (targeting the mRNAs [messenger RNAs] of invading organisms for destruction), or for identifying particular genes in a DNA sample.
2. The server has been used by molecular biologists and virologists to help predict conserved structural elements in the non-coding regions of gene transcripts that serve as signals that control expression levels of genes, or else the spatial and temporal expression of genes.
3. The server has been used by researchers in evolutionary biology to predict structures that are conserved during evolution.
4. The server is very popular with educators in bioinformatics who assign problems to students that require then to fold molecules on the server and to interpret the results.

I became aware of the so-called "RNA folding problem" many years ago and was asked to implement an existing computer program to compute foldings with minimum free energies. I soon realized that I could design a much better algorithm. Work has continued because I still find intellectual challenges in it and because the results are still in great demand and thus are highly cited.