Sites of interest on the World Wide Web—edited by David Roman

Modern Day Orphanages

In this month’s MI, Stanley Scheindlin writes on the history and current state of orphan drugs, orphaned patients, and rare diseases. The article outlines the interesting story of the development of some drugs for rare diseases, and the impact of the Orphan Drug act on that front. The FDA maintains a Web site for the Office of Orphan Product Development, (www.fda.gov/orphan/index.htm) that provides information on orphan product designation, tax credits, and orphan product grant applications. This Web site serves as a great starting point for learning more about the products and diseases that are not commonly found in today’s headlines.

On the topic of rare diseases, the NIH’s Office of Rare Diseases (http://rarediseases.info.nih.gov) provides access to genetic information resources, patient support groups, research and clinical trials information, as well as funding opportunities for research focused on rare diseases. The NIH Rare Diseases Clinical Network (http://www.ncrr.nih.gov/clinical/rdcrn_studylist.asp) lists the clinical trials that “have been approved to open as of May 1, 2006.” Interested persons can locate where clinical studies on rare diseases are being undertaken in the US; the list is arranged alphabetically by city name, and it is worth noting “that each study is taking place at multiple [cities].” Finally, the National Organization for Rare Disorders, Inc. (http://www.raredisease.org) is a wonderful trove of information on rare disorders, including indices and databases on particular diseases, resource guides, clinical fellowship monies, and seed-money research grants, to name only a few things offered at this helpful Web site. This would be an excellent Web site for a concerned patient or family member to begin with.

Two Web Sites for Protein–Protein Interactions

PDZ domains are one of several well-characterized protein–protein interaction regions. Even within the family of PDZ domains, however, there are unique features that determine the specificity of the interactions. Keeping track of the interaction motifs, binding partners, and solved interaction structures is a significant undertaking. Fortunately for us, the curators of the PDZbase at the Institute for Computational Biomedicine at Weill Medical College (Cornell University) have collated information and experimental results for over 300 of these protein–protein interactions. The PDZBase Web Service (http://icb.med.cornell.edu/services/pdz/start) provides easy search capabilities by PDZ name, accession number, ligand name, sequence motif, and position/residue queries.

Furthermore, once an interaction, PDZ domain, or ligand is identified, a graphical representation is presented, along with the appropriate literature references. The protein interaction representation alone provides a large amount of information about the interaction, while keeping the presentation clear. If you have any interest in protein-protein interactions, and PDZ domains in particular, this site should be at the top of your search list. Ten points if you can remember what the acronym PDZ stands for….

Another Web site for examining protein–protein interactions without a particular motif in mind is the MIPS Mammalian Protein-Protein Interaction Database (http://mips.gsf.de/proj/ppi/). This database provides a simple Boolean search to either input two proteins and search for known interactions, or simply to input a single favorite protein and examine what other players it may interact with in the complex network of signaling or structural assembly. This database is curated by the Munich Information Center for Protein Sequences (http://mips.gsf.de/), and even offers a complete download of the interaction database for scientists who agree to the terms of use.

Science in the Blogosphere

In this edition of MI, NetResults is presenting a notable first, and it’s about time––well, actually, it’s about a blog––the first one that has been featured in this column. Derek Lowe is an industrial medicinal chemist who writes about many informative and entertaining topics in his In the Pipeline blog (http://www.corante.com/pipeline). His blog entries run the gamut from commentary on recent pharmaceutical developments to the aftermath of clinical trials gone awry. Other recent entries focus on the issue of drug patents (and commentary on an upcoming book on that topic) as well as “Six Chemgeek questions” that provide food for thought, and some laughs to boot. Lowe’s blog entries are succinct and thought provoking, well-written and entertaining. This is one blog worth keeping and eye on, and it has made a home in my bookmarks folder. I think most of the MI readership will enjoy it as well, but whether you agree with Lowe’s assertions or not, there is a spot for your own commentary after each blog entry.