In silico Prediction of Deleterious Single Amino Acid Polymorphisms from Amino Acid Sequence

被引：4

作者：

Li, Shuyan ^{[1
,2
]}

Xi, Lili ^{[1
,2
]}

Li, Jiazhong ^{[1
,2
]}

Wang, Chengqi ^{[1
,2
]}

Lei, Beilei ^{[1
,2
]}

Shen, Yulin ^{[3
]}

Liu, Huanxiang ^{[4
]}

Yao, Xiaojun ^{[1
,2
]}

Li, Biao ^{[5
]}

机构：

[1] Lanzhou Univ, State Key Lab Appl Organ Chem, Lanzhou 730000, Peoples R China

[2] Lanzhou Univ, Dept Chem, Lanzhou 730000, Peoples R China

[3] Super Comp Ctr Gansu Prov, Lanzhou 730000, Peoples R China

[4] Lanzhou Univ, Sch Pharm, Lanzhou 730000, Peoples R China

[5] Indiana Univ, Sch Informat & Comp, Bloomington, IN 47408 USA

来源：

JOURNAL OF COMPUTATIONAL CHEMISTRY | 2011年 / 32卷 / 07期

基金：

中国国家自然科学基金;

关键词：

disease-related amino acid substitutions; protein sequence features; random forest; NUCLEOTIDE POLYMORPHISMS; FUNCTIONAL CONSEQUENCES; PROTEIN MUTATIONS; RANDOM FOREST; DISEASE; DATABASE; HYDROPHOBICITY; ASSOCIATION; RESOURCE; DESIGN;

D O I：

10.1002/jcc.21701

中图分类号：

O6 [化学];

学科分类号：

0703 ;

摘要：

Molecular cause of human disease retains as one of the most attractive scientific research targets for decades. An effective approach toward this topic is analysis and identification of disease-related amino acid polymorphisms. In this work, we developed a concise and promising deleterious amino acid polymorphism identification method SeqSubPred based on 44 features solely extracted from protein sequence. SeqSubPred achieved surprisingly good predictive ability with accuracy (0.88) and area under receiver operating characteristic (0.94) without resorting to homology or evolution information, which is frequently used in similar methods and usually more complex and time-consuming. SeqSubPred also identified several critical sequence features obtained from random forests model, and these features brought some interesting insights into the factors affecting human disease-related amino acid substitutions. The online version of SeqSubPred method is available at montana.informatics.indiana.edu/cgi-bin/seqmut/seqsubpred.cgi (C) 2010 Wiley Periodicals, Inc. J Comput Chem 32: 1211-1216, 2011

引用

页码：1211 / 1216

页数：6

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