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

作　　者：LV Qiang WU HongJie WU JinZhen HUANG Xu LUO XiaoHu QIAN PeiDe 

机构地区：[1]School of Computer Science and Technology, Soochow University [2]Jiangsu Provincial Key Lab for Information Processing Technologies [3]School of Electronic and Information Engineering, Suzhou University of Science and Technology

出　　处：《Science China(Information Sciences)》2013年第10期226-238,共13页中国科学（信息科学）（英文版）

基　　金：supported by National Natural Science Foundation of China(Grant No.60970055)

摘　　要：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 modells selected by our approach are the best of the published CASP8 results, and seven out of the modells 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 1] out of the modells are ranked in the top 10.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 modells selected by our approach are the best of the published CASP8 results, and seven out of the modells 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 1] out of the modells are ranked in the top 10.

关 键 词：protein backbone prediction PARALLEL ant colony optimization 

分 类 号：Q51[生物学—生物化学]