Originally posted by Scott Jensen
Also, what's "Gaussian" and what does the "A" in say 6A mean? And while I'm asking, could you also explain the "why" of the following: "...but the important quantity is the TOTAL number of structures made by everybody altogether."
Lastly, can I get a college credit in computational biology for reading this forum?
Ok, hope i can help a bit... first of all, the A. The "A" is for angstroms (its a very small unit of length - a ten billionth of a meter). we measure the difference between the protein generated and the "real" one, the structure that appears in nature. when we talk about a structure having a 4A RMSD (root mean squared deviation) that means that the structure generated deviates from the real structure by an average of 4 angstroms. basically the smaller the RMSD is, the closer the generated structure is to the real one.
next, Gaussian. A Gaussian or "normal" probability distribution is a fancy way of saying a bell curve. remember algebra 2 from high school? Basically you have the mean or average in the middle, where most things are, and it falls off on either side (most things are in the middle near the average, and the farther out you go from the average, the fewer you get) Many random things fall into a gaussian distribution because that's what kind of curve you tend to get when you have a lot of independent random variables working together and you add them up (it's been proven). Probably all the structures generated taken together make up a Gaussian distribution.
An extreme value distribution is the kind of distribution you get when you take, for example, the largest value out of each of a lot of sets. To use howard's example, if you took the tallest person out of each class at a college, or the smallest RMSD out of each set of proteins. The result is a different kind of statistical distribution, which to the untrained eye (like mine, heh) looks vaguely like a gaussian bell curve, but isn't.
Attached is a picture of some extreme value distributions (where the minimum was taken), from http://www.itl.nist.gov/div898/handb...on1/apr163.htm
if you are familiar with gaussian bell curves you may notice that unlike the gaussians, these shapes are asymmetric, but like gaussians, can have varying degrees of "spread-out-ness" (standard deviation).
As for "...but the important quantity is the TOTAL number of structures made by everybody altogether."
I think what Howard meant is that it doesnt matter how many any individual person produces, whats important is how much everyone together produces, since they all end up in the same pot anyway. it makes sense to think that since the structures are sorta randomly generated, that the more you generate, the better your odds of getting good ones (kinda like having lots of lottery tickets gives you better odds of winning).
computational biology? nope, you just got a crash course in statistics
whew. hope that helps
Basically you have the mean or average in the middle, where most things are, and it falls off on either side (most things are in the middle near the average, and the farther out you go from the average, the fewer you get) Many random things fall into a gaussian distribution because that's what kind of curve you tend to get when you have a lot of independent random variables working together and you add them up (it's been proven). Probably all the structures generated taken together make up a Gaussian distribution.
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