Slashdot Mirror
VigyaanCD: Bio/Chemical Modeling Workbench on PC
PKA writes "Announcing the release of VigyaanCD (homepage, mirror1,
mirror2). Vigyaan, a Knoppix customization, is an electronic
workbench for computational biology and
computational chemistry. The user can choose from
more than 20 science applications. In addition to
bioinformatics software, it provides GROMACS,
TINKER for biomolecular modeling and Ghemical,
MPQC, PSI3 for quantum chemistry calculations.
VigyaanCD is a live Linux CD containing all the
software required to boot the PC into workbench
environment and is suitable both for beginners (12
demos and tutorials) and experts. Learning
computational biology/chemistry has never been
easier, so grab
the free ISO image from several mirrors around the
world and put your PC to work."
"OTH, do we really want anyone creating their very own designer drugs/poisons/catylists/etc?"
Sure we do. New drugs come from somewhere. Some are found using rational design, or are based on an initial hit from rational design. I'm working on a project right now to try and inhibit an enzyme that appears to be critical for establishment of a long-term infection of a certain major pathogen. One way of doing that is by taking the structure of the enzyme and trying to model in a whole series of compounds to find ones that appear to bind well to the active site. Another would be to attempt to solve the enzyme:inhibitor structure by x-ray crystallography, but crystallization's not always straightforward. Often the two methods are used in tandem.
"Maybe someone could explain whether or not it's possible to take a model and actually make a few grams of it."
Once you've got a model compound that you're interested in trying out in the real world, you're going to have to figure out how to obtain it. Various chemical and pharmaceutical companies (sigma, fisher, roche, or with all the consolidations lately is it sigmafisherrocheetc?) have hundreds of thousands (or more) compounds available for sale. Or you might be unlucky and have to make it. In that case, someone might have synthesized the compound for a completely different purpose already, in which case you might use a program such as Scifinder Scholar to search the organic chemistry literature to see if it's already been made. This program's not something that everybody has, my entire university's license only allows one person from the whole university to be logged on at a given time. If it's there, you're in luck and you "just" have to follow their materials and methods. Of course, it still could be a bitch. I've got a very bright undergrad working on synthesizing a compound for me that I found this way. In three months he's managed to get a trace amount that's highly impure--and this is with him working in an organic chemistry prof's lab with all the equipment and support necessary. If you're unlucky and it hasn't been synthesized or isn't in the literature, then you've got to figure the synthesis out yourself--which considering what the organic chemists have already made will likely require a hell of a lot of experience and expertise in chemistry to pull off--not just somebody out there in a basement lab. A basement lab might be just fine for synthesizing a number of previously known poisons or drugs, of course.
This may give you a limited working knowledge, but only formal education and real professional experience will provide you the depth of knowledge to become a competent bioinformatics programmer
Agreed. However, this seems like a good way to introduce the interested life scientist to Bioinformatics, or even Linux in general. Also, the CD appears to contain not just programming tools, but general purpose scientific applications which could be effectively used by life scientists even with no programming knowledge whatsoever.
As far as drug production, I say go for it, but note that this approach WILL NOT show you HOW to make the molecule. It's not a matter of figuring out what the compound should look like, it's a matter of testing it and making the damn thing in the first place. That's why pharmaceutical companies need so much money; they need the best chemists to figure out how to make all these exotic drugs without the use of poisonous reagents, and then they need to make sure the drugs work the way you want (they usually do not).
On that note, if you want to make a poison it's not just a matter of tossing molecules at a computer; you gotta know how your prospective poison is going to do the poisoning...never mind the testing and actually making it.