计算机科学 ›› 2015, Vol. 42 ›› Issue (3): 237-240.doi: 10.11896/j.issn.1002-137X.2015.03.049
郝小虎,张贵军,周晓根,程正华,张启鹏
HAO Xiao-hu, ZHANG Gui-jun, ZHOU Xiao-gen, CHENG Zheng-hua and ZHANG Qi-peng
摘要： 针对蛋白质构象空间优化问题,提出一种基于片段组装的构象空间优化算法。算法利用基于Rosetta粗粒度的知识能量模型有效地提高了收敛速度；同时,借助片段组装技术可以有效弥补因能量函数不精确而导致的预测精度不足的缺陷；此外,差分进化算法的引入使得算法具有较好的全局搜索能力。5种测试蛋白的实验结果表明,所提算法具有较好的搜索性能和预测精度。
| [1] Collins F,Patrinos A,Jordan E,et al.New goals for the US Human Genome Project[J].Science,1998-2003,282(5389):682-689 [2] 李娜.人类基因组计划十年反思[J].科技导报,2010,8(13):11 [3] 黄俊峰,段鹏,吴文言.基于模板的蛋白质结构预测[J].生物物理学报,2011,7(1):28-37 [4] Werner T,Morris M B,Dastmalchi S,et al.Structural modeling and dynamics of proteins for insights into drug interactions[J].Advanced Drug Delivery Review,2012,64(4):323-343 [5] Lee J,Joo K,Kim I,et al.Prediction of protein tertiary structure using PROFESY,a novel method based on fragment assembly and conformational space annealing[J].Proteins:Structure,Function,and Bioinformatics,2004,56(4):704-714 [6] Bradley P,Misura K M,Baker D.Toward high-resolution de no-vo structure prediction for small proteins[J].Science,2005,309(5742):1868-1871 [7] Lee J,Sasaki T N,Sasai M,et al.De novo protein structure prediction by dynamic fragment assembly and conformational space annealing[J].Proteins:Structure,Function,and Bioinformatics,2011,79(8):2403-2417 [8] Lee J.Exact Enumeration of Protein Conformations from Fragment Assembly[J].Journal of Physics:Conference Series,2013,410:1-5 [9] Lee J,Wu S,Zhang Y.Ab initio protein structure prediction[M]∥ From Protein Structure to Function with Bioinformatics,2009:3-25 [10] Saleh S,Olson B,Shehu A.A population-based evolutionarysearch approach to the multiple minima problem in de novo protein structure prediction[J].BMC Structural Biology,2013,13(1):1-28 [11] Rohl C A,Strauss C E,Misura K M,et al.Protein structure pre-diction using Rosetta[J].Numerical Computer Methods,2004,383:66-93 [12] Kortemme T,Morozov A V,Baker D.An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes[J].Journal of molecular biology,2003,326(4):1239-1259 [13] Handl J,Knowles J,Baker D,et al.The dual role of fragments in fragment-assembly methods for de novo protein structure prediction[J].Proteins:Structure,Function,and Bioinformatics,2012,80(2):490-504 [14] Handl J,Knowles J,Baker D,et al.The dual role of fragments infragment-assembly methods for de novo protein structure prediction[J].Proteins:Structure,Function,and Bioinformatics,2012,80(2):490-504 [15] Kolodny R,Koehl P,Guibas L,et al.Small libraries of protein fragments model native protein structures accurately[J].Journal of Molecular Biology,2002,323(2):297-307 [16] Storn R.Differential evolution design of an IIR-filter[C]∥ Proceedings of IEEE International Conference on Evolutionary Computation,1996.Nagoya,1996,268-173 [17] 程正华,张贵军,邓勇跃,等.一种新的蛋白质结构预测多模态优化算法[J].计算机科学,2013,40(9):212-215,229 [18] Wang G,Dunbrack R L.a protein sequence culling server[J].Bioinformatics,2003,19(12):1589-1591 [19] Gront D,Kulp D W,Vernon R M.Generalized Fragment Picking in Rosetta:Design,Protocols and Applications[J].PLoS One,2011,6(8):e23294 |
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