• Key
• Strong Points
• Weak Points
• Ratings
• Excellent
• Very Good
• Good

• Easy-to-use, nice variety of graphics
• Login glitches
• Rating

• Pathway Builder Online
• www.proteinlounge.com/PBTool/ListPathwayThumb.aspx

• Do you get excited over beautiful, colorful molecular pathways? (Do you collect the free pathway posters at vendor shows and decorate your office or apartment with them? Be honest, now.) Well now you can do one better than simply collect pathway posters—you can make them yourself! Pathway Builder Online is a simple-to-use application through ProteinLounge.com. In addition to the many pathway templates that it provides, the application allows users to select the desired cell, organelle, and molecules to include in the pathway. Easy click-and-position graphics include a variety of colorful ion channels, arrows, and many other animated components. You can add your own text and save your creations. All that is required is registration on the site (it’s free). I did find that the login on the site is a bit glitchy, so you might have to resort to accessing the page from the confirmation e-mail you’ll receive upon registration.

• Nice organization, different search functions
• Nothing major
• Rating

• SNPper
• snpper.chip.org/bio/snpper-enter

• First off, let me just say that when you click onto this site, the username is “guest”, and the password field is left blank. (In reading that first sentence, you have just saved yourself a lot of frustration.) SNPper is a database of single nucleotide polymorphisms (though I happen to think that it would make a great name for a barber shop, as well). There is no shortage of SNPs in this database—it houses 9,163,169 to be exact—and there are multiple ways to use this online resource. You can search by the name of the SNP, by position on a specific chromosome, or you can input a name of a gene to find all known SNPs associated with it.  There is a fair amount of background information on the site, including how the database was constructed and what types of data are included. As an added bonus, the website includes other analysis tools such as the GeneOntology browser and amino acid properties table.

• Variety of analysis tools
• Nothing significant
• Rating

• SuperFamily
• supfam.mrc-lmb.cam.ac.uk/SUPERFAMILY

• I guess I’m not altogether protein-minded, as the title of this site evokes images of in-laws, a family Christmas dinner, and sibling quarrels when I look at it. To perhaps your relief, this site has nothing to do with human familial relations, but rather those of structural and functional proteins. SuperFamily is a database of annotations for these proteins in all completely sequenced organisms. The term “superfamily” refers to a group of protein domains from different families that have a common evolutionary ancestor. Users can submit a protein or DNA sequence for family and superfamily level classification, view genome statistics, and display phylogenetic trees, to name just some of the features of the website. There is nothing fancy about the website, but there are many useful analysis tools hidden among the simple page text.

• Easy-to-use, links directly to primary literature
• None
• Rating

• Therapeutic Targets Database
• xin.cz3.nus.edu.sg/group/CJTTD/TTD.asp

• The ultimate goal of biomedical research is to apply newfound knowledge of the human body and disease toward the development of novel therapies. The Bioinformatics and Drug Design Group at the National University of Singapore offers a wonderful online access point to the world of drug design, the Therapeutic Targets Database (TTD). The TTD is the type of database one loves to explore. It doesn’t matter if you’re searching for a drug, a disease, a target protein, or a metabolic pathway—just type your query into the search field. It’s as simple as that. The TTD excels in combining these various search parameters as well as in linking scientists directly to the literature. Once the search results are displayed and the target of interest selected, a great deal of information is provided, including literature references. These references are linked to PubMed, so inquirers can directly access the primary literature from the TTD’s website.

• Reader-friendly, accessible by a wide audience
• None
• Rating

• Understanding Cancer
• www.cancer.gov/cancertopics/understandingcancer

• Cancer has sadly become a fixture in today’s society, and with its prevalence comes the medical vernacular: metastasis, angiogenesis, routine screenings, radiation therapies, and on, and on. If you find yourself getting lost in it all (and you’re not alone), be sure to take advantage of the National Cancer Institute’s “Understanding Cancer” series. There are 14 topics in the series, ranging from blood stem cell transplants to HPV vaccine, and each topic comes in the form of presentation slides and accompanying notes. For some of the topics, the powerpoint presentation or pdf can be downloaded. The information is accessible for anybody interested in learning more about cancer, from the general public, to science students, to scientists. The colorful, graphic-rich slides are both interesting and informative, shedding light on topics that you might often hear on the news, but you may not fully understand in the context of today’s medical climate.

• Nice web design and organization
• None
• Rating

• World Register of Marine Species (WoRMS)
• www.marinespecies.org/index.php

• Quick—get out a piece of paper and a pencil, and name as many marine species as you can. (There’s nothing like a good ol’ pop quiz, is there?) Did you find yourself getting stuck after whale, dolphin, and starfish? Then perhaps you should click over to WoRMS, which (oddly enough) is not about worms at all. Rather, this ambitious project—the World Register of Marine Species—aims to provide a comprehensive list of names of marine organisms that can be used to interpret taxonomic literature. The register currently contains 147,097 valid species names, but the goal is to obtain all of the estimated 230,000 marine species by next year. Visitors can search WoRMS by either common or scientific name to find the taxon details for that species. Even if you have no interest in oceanic taxonomy, there is a great photo gallery of various species (though nowhere near 147,097 of them).

*The opinions expressed are solely those of the author(s) and should not be construed as reflecting the viewpoints of the publisher, Genetic Engineering & Biotechnology News, Mary Ann Liebert, Inc., the publishing house, or employees and affiliates thereof.

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