Marcia Soriano: CASP6 Protein Structure Prediction

CASP, Critical Assessment of Techniques for Protein Structure Prediction, is an experiment that involves determining protein structure given an amino acid sequence using computational methods. The goal of this experiment is "to obtain an in-depth and objective assessment of our current abilities and inabilities in the area of protein structure prediction". During the months of May through August, different amino acid sequences ('targets') are released on the CASP website weekly. CASP participants must meet the given target deadline to submit their protein structure. Sometime after the target deadline, the actual protein structure (determined by experimental methods, i.e. NMR, x-ray crystallography) is released to the public. At the end of the year, a conference is held to assess the results of the participants. This year the conference will be held at Gaeta, Italy from December 4-8. We participated in the CASP6 protein structure prediction experiment. I was involved in targets T0239 and T0226. In order to solve the structure of a protein given it's amino acid sequence, we used three different methods depending on the clues we can find. We used the SAM server to help find the clues and the Undertaker program to build a predicted protein structure. We have yet to determine the outcome of the experiment as the conference to assess our results takes place in December.