MMDB

One of the things that drives me crazy on occasion is nomenclature. Well, maybe not just nomenclature, it's really the continual changes in the nomenclature, and the time it takes for those changes to ripple through various databases and get reconciled with other kinds of information. And the realization that sometimes this reconciliation may never happen. One of the projects that I've been working on during the past couple of years has involved developing educational materials that use bioinformatics tools to look at the isozymes that metabolize alcohol. As part of this ... Read more
Instead of enjoying a sunny summer day today, or partying with SciBlings in New York, I'm staring out my window watching the rain. Inspiration hit! What about searching for August? i-15229e4ef21ba40ef0a2aa526c93f358-HFQ_protein.gifFolks, meet the HFQ protein from E. coli. I found this lovely molecule by doing a multi-database search at the NCBI with the term 'August'. HFQ is a lovely protein with ... Read more
Over 2600 genetic diseases have been found where a change in a single gene is linked to the disease. One of the questions we might ask is how those mutations change the shape and possibly the function of a protein? If the structures of the mutant and wild type (normal) proteins have been solved, NCBI has a program called VAST that can be used to align those structures. I have an example here where you can see how a single amino acid change makes influenza resistant to Tamiflu®. This 4 minute movie below shows ... Read more

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