A parallel ant colonies approach to de novo prediction of protein backbone in CASP8/9

Predicting the three-dimensional structure of proteins from amino acid sequences with only a few remote homologs, or de novo prediction, remains a major challenge in computational biology. The modeling of the protein backbone represents the initial phase of a protein structure prediction process. Using a parallel ant colony optimization based on sharing one pheromone matrix, this report proposes a parallel approach to predict the structure of a protein backbone. The parallel approach combines various sources of energy functions and generates protein backbones with the lowest energies jointly determined by the various energy functions. All free modeling targets in CASP8/9 are used to evaluate the performance of the method. For 13 targets in CASP8, two out of the predicted model1s selected by our approach are the best of the published CASP8 results, and seven out of the model1s are ranked in the top 10. For 29 targets in CASP9, 20 out of the best models from our predictions are ranked in the top 10, and 11 out of the model1s are ranked in the top 10.