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

• Listings
• Rather schizo in its approach
• Rating

• Biology Jobs
• www.biologyjobs.com
• Way back in the early days of this column (1998), I was one of the first reviewers to report on this well-designed, educational page. It seemed like now might be a good time to provide an update. Put together by Fred Senese at Frostburg State University, the site excels in several areas. The first is a common compound library. In it, users enter the name of a compound and a search engine retrieves data about the molecule, which includes links to PubChem, Webbook, and MSDS info. Chime structures and spectra are included where relevant. Second is a section entitled Exam Survival Guide. It provides practice exams and “ten ways to pass your next exam” that will be popular with students. A glossary covers many of the terms and can be sorted by topic. Last, a set of Construction kits help students to “build” chemical equations, convert units, and construct ionic compounds. Clearly a labor of love, General Chemistry Online has been around long enough to be called a classic of web education.

• Interesting mix of info
• Ugly, weak in places
• Rating

• Bioplanet
• www.bioplanet.com/index/php
• Billing itself as the “bioinformatics homepage,” BioPlanet could probably win some kind of an award for a gaudy opening page. From the cheap looking ringed planet to the visually unattractive mix of blue underlined links, orange headings, and occasional splashes of yellow for emphasis, beauty is more than skin deep here. There is a lot more to the site than the ugliness that meets the eye. Start with the job listings (over 1,400 jobs), resume listings (740), news links, stock market reports, and numerous forums, there is something here for almost anyone. The job listing was one place, however, where the delivery was a bit less than one might expect. Many of the jobs were simple writing opportunities with dreadful pay—$5–$8 per page. To be sure, there were some professional bioinformatics-related jobs, including several for programmers, but they were a small percentage of the 1,400 listed. All in all, BioPlanet hits in a few places and misses in a few others. It would not take much, however, to make this an outstanding site, so I hope the developers will keep working on it.

• Great design, useful for students
• None
• Rating

• General Chemistry Online
• antoine.frostburg.edu/chem/senese/101/index.shtml
• Way back in the early days of this column (1998), I was one of the first reviewers to report on this well-designed, educational page. It seemed like now might be a good time to provide an update. Put together by Fred Senese at Frostburg State University, the site excels in several areas. The first is a common compound library. In it, users enter the name of a compound and a search engine retrieves data about the molecule, which includes links to PubChem, Webbook, and MSDS info. Chime structures and spectra are included where relevant. Second is a section entitled Exam Survival Guide. It provides practice exams and “ten ways to pass your next exam” that will be popular with students. A glossary covers many of the terms and can be sorted by topic. Last, a set of Construction kits help students to “build” chemical equations, convert units, and construct ionic compounds. Clearly a labor of love, General Chemistry Online has been around long enough to be called a classic of web education.

• Interface, great idea
• Implementation unclear
• Rating

• Organelle Map Database
• proteome.biochem.mpg.de/ormd.htm
• A distinguishing feature of eukaryotic cells over their prokaryotic counterparts is the presence in the former of organelles, and it is these membrane-enclosed structures that are at the root of cell biology and this informative website. Going beyond the organelle, molecular biologists have been busy over the years mapping the movement of proteins into and through these various structures and this data provides the fodder for the Organelle Map Database (ORMD). The opening page provides a simple, visual map of a eukaryotic cell. Visitors can click on an organelle to (presumably) see a list of proteins associated with that structure. When I clicked on Golgi apparatus, I got a list of 257 proteins. Clicking on links for several of these brought up additional sequence-related info. I was puzzled, though, in that I couldn’t find Golgi referenced for several of the genes I selected. Is the database inaccurate? Are the sequence databases linked to incomplete? I don’t know. There is an online Cell paper (subscription required) referenced at the site, and it probably has the answers. I don’t, but neither do I think I should have to search for them at a site like this.

• Simple organization
• Missing links in places
• Rating

• Plasma Proteome Database
• www.plasmaproteomedatabase.org
• Proclaiming itself as “the first of its kind,” the Plasma Proteome Database aims to be a comprehensive resource for plasma proteins in human beings. With over 7,500 proteins and isoforms, the site may well live up to its billing. The main focus of the site is providing easy access to information, and with this in mind, visitors are provided with options to Browse by molecule function, domains, motifs, post-translational modification, and cellular organelle component. Within these categories are individual links to additional information, though the molecular function category had many functions with no link and thus no description. The other option at the site is the Query selection, which allows users to search by protein name, gene symbol, molecular function, and eight other criteria. Though the site is simple in design, it seems to present enough options to users for it to achieve its goal.

• Useful sites, easy access
• None
• Rating

• Research Tools
• www.nih.go.jp/~jun/research
• This site looked familiar to me, but I couldn’t find its URL or any name like it in my database. Perhaps they’ve simply used a coloring scheme like another site covered here before, or (more likely) they have bought an old site, renamed it, and given it a new URL. Either way, they have a winner on their hands. With a focus on online research tools useful for molecular biologists, Research Tools is appropriately named and poised to handle a lot of requests. The site is organized in a frame format. The left, top panel provides a table of contents with links that, when clicked, bring up an appropriate set of links in the right panel. Jun Ishikawa, who appears to have put this together (English and Japanese versions), has spent a lot of time picking relevant links for molecular biological researchers. Indeed, I’ve bookmarked it in my browser to allow me easy access to hundreds of useful sites.

• Ambitious idea
• Still in development
• Rating

• The Ribosome Builder Project
• rbuilder.sourceforge.net
• Virtual life projects have been around since the early days of personal computing. As computers have gotten more sophisticated, so too have these applications. An interesting cousin of these efforts is the subject of this rather unusual site, The Ribosome Builder Project. Aiming to design a software program to simulate structural models of the macromolecules comprising the ribosome, along with a simple molecular dynamics approach that keeps an eye on bond lengths, angles, and steric exclusions, the Ribosome Builder Project may be an important step in actually modeling a single cell. A program has, in fact, been released by the site’s designer, William Knight, and it can be downloaded from the site. As an open-source project, the software can be expected to grow and improve with time. If you’re a programmer and are interested in modeling living systems, this is a must see.

• Good coverage of topic
• Too little information about tmRNA
• Rating

• tmRDB Welcome
• psyche.uthct.edu/dbs/tmRDB/tmRDB.html
• tmRNAs are bacterial molecules that have been described as a cross between tRNAs and mRNAs. They are implicated in the unusual process of trans-translation, which involves ribosomal switching between translation of a truncated mRNA and the tmRNA that invades it when translation is blocked. The resulting polypeptide gains a few amino acids from the tmRNA that targets it for destruction. Trans-translation probably plays a role in keeping ribosomes functioning and preventing the accumulation of undesired translation products. The tmRDB database provides access to sequence information about the tmRNAs known across the bacterial kingdom, as well as sequences of proteins associated with tmRNAs. The list of the former is extensive, indicating the importance of these molecules for bacterial survival. Structures, models, and links round out the site. My only complaint is the site’s limited description of tmRNAs.

*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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