Search:

Structure prediction has been shown to be NP-complete 10 years ago:

Ngo, JT and Marks, J. Protein Eng. 1992; 5:313-321.

Incidentally, the concept of NP-complete-ness was developed right here...

You've got most of it right (more or less) :p .
The major bias we use right now is something very old and fairly simple, called "secondary structure prediction". If you look at a bunch of protein...

Raj brings up some valid points which we should certainly address. We are doing "real" science here. As Aegion says however, it is clear (at least to me) that Raj has not had a good look at our...

I will just make a few more brief comments in response to the above discussion.

There is more to our method than random sampling and then scoring afterwards. We have ways to reduce the search...

Raj,

(Yes it is Howard, Brian the Fist is just an alias). You are correct that we are indeed dealing with sampling. But we are NOT using the native structures to help us predict in any way.You...

I will pipe in here to answer some of Raj's questions (and they are good questions which he poses).

Firstly, if you wish to learn more about the algorithm and our approach please check out the...