P.C. Shannon

I�m through the first version of my bioinformatics program for my first rotation. The results are disappointing, but you can take a look at some of them here. (You�ll need the Chime browser plug-in.) One problem lies in trying to calculate distances in three-dimensional space between a nucleotide and an amino acid that is hydrogen-bonded to it. Another problem is trying to figure out possible orientations for the amino acid that would still satisfy distance and H-bond requirements. I did some thinking on these topics yesterday, made some sketches, and then tried to do some research on 3D math on the internet. It turns out a lot of this stuff has already been worked out — a lot of it by people who do computer animation and graphics — so I don�t have the reinvent the wheel. The bad part is that it�s all horribly horribly complex. And involves vector math. Which I don�t remember. So I think I�m going to do a little more fine tuning on this algorithm, which should make it more accurate — and hopefully yield some interesting data — before moving on to other approaches that, again, will hopefully give me some really interesting results.