Simons, K.T., Bonneau, et al.  Proteins 3, 171-176 (1999)

To generate structures consistent with both the local and non-local interactions responsible for protein stability, 3 and 9 residue fragments of known structures with local sequences similar to the target sequence were assembled into complete tertiary structures using a Monte Carlo simulated annealing procedure (Simons, K.T. et al., J. Mol. Biol., 268:209-25, 1997 [Full Text PDF]). The scoring function used in the simulated annealing procedure consists of sequence dependent terms representing hydrophobic burial and specific pair interactions such as electrostatics and disulfide bonding, and sequence independent terms representing hard sphere packing, alpha-helix and beta-strand packing and the collection of beta-strands in beta-sheets [Simons, K.T. et al., Proteins, 34:82-95, 1999 ]. For each of 21 small, ab initio targets, 1200 final structures were constructed, each the result of 100,000 attempted fragment substitutions. The five structures submitted for the CASP III experiment were chosen from the ~25 structures with the lowest scores in the broadest minima (assessed through the number of structural neighbors, Shortle, D., et al., PNAS, 95:1158-62, 1998 [Full Text PDF]). The results were encouraging: highlights of the predictions include a 99 residue segment (target 79) for MarA with an rmsd of 6.4 angstroms to the native structure, a 95 residue (full length) prediction for the EH2 domain of EPS15 (target 74) with an rmsd of 6.0 angstroms, a 75 residue segment of DNAB helicase (target 56) with an rmsd of 4.7 angstroms, and a 67 residue segment of ribosomal protein L30 (target 77) with an rmsd of 3.8 angstroms. These results suggest that ab initio methods may soon become useful for low resolution structure prediction for proteins which lack a close homologue of known structure.