A novel method for ab initio prediction of protein
tertiary structures, PROFESY (PROFile Enumerating SYstem), is
proposed. This method utilizes the secondary structure prediction
information of a query sequence and the fragment assembly
procedure based on global optimization. Fifteen residue long
fragment libraries are constructed using the secondary structure
prediction method PREDICT, and fragments in these libraries are
assembled to generate full-length chains of a query protein.
Tertiary structures of 50 to 100 conformations are obtained by
minimizing an energy function for proteins, using the
conformational space annealing method that enables one to sample
diverse low-lying local minima of the energy. We apply PROFESY for
benchmark tests to proteins with known structures to demonstrate
its feasibility. In addition, we participated in CASP5 and applied PROFESY
to four new fold targets for blind prediction. The results are
quite promising, despite the fact that PROFESY was in its early
stages of development. In particular, the PROFESY successfully
provided us the best model-one structure for the target T0161.