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采用伪氨基酸组成预测水解酶亚家族

DOI: 10.11830/ISSN.1000-5013.2010.03.0317

Keywords: 水解酶亚家族, 特征值, 伪氨基酸, k-近邻

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Abstract:

利用伪氨基酸组成提取蛋白序列特征值,考察参数λ和w对识别效果的影响,以k-近邻作为基础分类器,用于预测水解酶的亚家族类型.结果表明,伪氨基酸组成特征提取法与单纯的20个氨基酸组成特征方法相比,其识别精度有较大程度提高.20AA组成的平均预测精度为72.3%,而伪氨基酸组成特征提取的识别效果可达82.7%.在参数影响考察方面,自相关性函数个数的选取对识别效果影响较大,而权重因子w对识别效果影响则很小.

References

[1]  BAIROCH A, APWEILER R. The SWISS-PROT protein sequence data bank and its supplement TrEMBL [J]. Nucleic Acids Research, 2000(1):31-36.doi:10.1093/nar/25.1.31.
[2]  段作纬, 熊郁良, 陈训如. 用胰蛋白酶和糜蛋白酶急救药盒救治毒蛇咬伤256例 [J]. 中国危重病急救医学, 1998(6):336-338.
[3]  VIIKARI L, PAUNA M, KANTELINEN A. Bleaching with enzymes with enzymes [A]. Stockholm:Swedish Pulp and Paper Research Institute, 1986.67-69.
[4]  CLASSEN H L. Cereal grain starch and exogenous enzymes in poultry diets [J]. Animal Feed Science and Technology, 1996(1):21-27.doi:10.1016/S0377-8401(96)01002-4.
[5]  ALTSCHUL S F, MADDEN T L, SCHAFFER A A. Gapped BLAST and PSI-BLAST:A new generation of protein database search programs [J]. Nucleic Acids Research, 1997, (17):3389-3402.
[6]  COVER T M, HART P E. Nearest neighbor pattern classification [J]. IEEE Transactions on Information theory, 1967(1):21-27.
[7]  CUI J, HAN L Y, LIN H H. Prediction of MHC-binding peptides of flexible lengths from sequence-derived structural and physicochemical properties [J]. Molecular Immunology, 2007(5):866-877.doi:10.1016/j.molimm.2006.04.001.
[8]  张光亚, 葛慧华, 方柏山. 采用BP算法的多层感知机模型的蛋白识别 [J]. 华侨大学学报(自然科学版), 2009(2):161-165.
[9]  GUO Yan-zhi, LI Meng-long, ZOU Xiao-yong. Fast fourier transform-based support vector machine for prediction of G-protein coupled receptor subfamilies [J]. ACTA BIOCHIMICA ET BIOPHYSICA SINICA, 2005, (11):759-766.
[10]  CHOU K C. Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes [J]. BIOINFORMATICS, 2005(1):10-19.doi:10.1093/bioinformatics/bth466.
[11]  BAIROCH A, APWEILER R, WU C H. The universal protein resource (uniprot) [J]. Nucleic Acids Research, 2005():154-159.
[12]  丁彦蕊, 蔡宇杰, 须文波. 基于氨基酸组成预测蛋白质热稳定性的v-支持向量机方法 [J]. 计算机与应用化学, 2005(6):51-57.doi:10.3969/j.issn.1001-4160.2005.06.006.
[13]  GROMIHA M M, AHMAD S, SUWA M. Application of residue distribution along the sequence for discriminating outer membrane proteins [J]. Computational Biology and Chemistry, 2005(2):135-142.doi:10.1016/j.compbiolchem.2005.02.006.
[14]  CHOU K C. Prediction of protein cellular attributes using pseudo-amino-acid-composition [J]. Structure Function and Genetics, 2001(3):246-255.doi:10.1002/prot.1035.
[15]  BAIROCH A. The ENZYME database in 2000 [J]. Nucleic Acids Research, 2000(1):304-305.
[16]  CHOU K C. Prediction of protein cellular attributes using pseudo-amino-acid-composition [J]. Proteins:Structure, Function, and Genetics, 2001(3):246-255.doi:10.1002/prot.1035.
[17]  TANFORD C. Contribution of hydrophobic interactions to the stability of the globular conformation of proteins [J]. Journal of the American Chemical Society, 1962, (22):4240-4247.doi:10.1021/ja00881a009.
[18]  HOPP T P, WOODS K R. Prediction of protein antigenic determinants from amino acid sequences [J]. Proceedings of the National Academy of Sciences(USA), 1981(6):3824-3828.doi:10.1073/pnas.78.6.3824.
[19]  INAMDAR N M, EHRLICH K C, EHRLICH M. Data mining in bioinformatics using Weka [J]. Bioinformatics, 2004, (15):2479-2481.doi:10.1093/bioinformatics/bth261.
[20]  QIU Jian-ding, LIANG Ru-ping, ZOU Xiao-yong. Prediction of protein secondary structure based on continuous wavelet transform [J]. Talanta, 2003(3):285-293.doi:10.1016/S0039-9140(03)00278-9.

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