In silico prediction of deleterious single amino acid polymorphisms from amino acid sequence

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 aci...

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Bibliographic Details
Published in:Journal of computational chemistry 2011-05, Vol.32 (7), p.1211-1216
Main Authors: Li, Shuyan, Xi, Lili, Li, Jiazhong, Wang, Chengqi, Lei, Beilei, Shen, Yulin, Liu, Huanxiang, Yao, Xiaojun, Li, Biao
Format: Article
Language:English
Subjects:
Accuracy
Amino Acid Sequence
Amino Acid Substitution
Amino acids
Analytical chemistry
Computational Biology
Computer Simulation
Databases, Protein
disease-related amino acid substitutions
Extraction processes
Humans
Polymorphism
Polymorphism, Single Nucleotide
protein sequence features
Proteins
Proteins - chemistry
Proteins - genetics
random forest
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Summary: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 © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011
ISSN:0192-8651
1096-987X
DOI:10.1002/jcc.21701