Understanding and predicting protein structure

Protein structure prediction from sequence remains a premiere computational problem for modern molecular biology. Just as protein structure prediction may be divided into sub-problems of main-chain and side-chain placement, so the protein structure prediction track this year has been divided into sub-tracks of protein threading (organized by Daniel Fischer and Adam Godzik) and side-chain packing (organized by Su Chung and S. Subbiah). The result is an unusually rich tour through di erent levels of protein structure prediction, from coarse-grained prediction of the tertiary fold to the ne-grained atomic detail of individual side-chains. 1 Protein Threading Organized by Daniel Fischer and Adam Godzik. All threading and folding algorithms depend crucially on the quality of the energy parameter set. For many years such sets were built by analyzing interaction regularities in known protein structures. Despite a long history of such derivations, fundamental problems with the theoretical background persist till today, with many existing derivations containg important omissions