Archive for March, 2008

Book on parallel scientific computing

Friday, March 28th, 2008

There is a good book on parallel scientific computing. It is “Parallel scientific computing in C++ and MPI” by George Karniadakis and Robert Kirby. It is very C++ oriented and I found it very useful. Here are the Google Books and Amazon.
Unfortunately, I had to return it before I could fully explore it. :-(

Side-Chain Entropy

Thursday, March 6th, 2008

Side-chain calculation is a tricky business in protein folding community. Proteins pack not only backbones but also side chains. But due to its flexible nature, the folding community make much less progress on side-chain packing compared to backbone packing. Side-chain entropy is another concept that I just heard recently (it is actually an old “concept” though). As we saw in many fields, the complex side-chain entropy can be divided into two components, the vibrational and the conformational. The vibrational part varies very little if at all in the folded and unfolded states. Whereas the conformational is different, it actually plays critical roles in protein folding. Jinfeng Zhang and Jun Liu published a paper focusing on the side-chain conformational entropy.

To be continued.