iPTREE-STAB: interpretable decision tree based method for predicting protein stability changes upon mutations

We have developed a web server, iPTREE-STAB for discriminating the stability of proteins (stabilizing or destabilizing) and predicting their stability changes (ΔΔG) upon single amino acid substitutions from amino acid sequence. The discrimination and prediction are mainly based on decision tree coup...

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Veröffentlicht in:	Bioinformatics 2007-05, Vol.23 (10), p.1292-1293
Hauptverfasser:	Huang, Liang-Tsung, Gromiha, M. Michael, Ho, Shinn-Ying
Format:	Artikel
Sprache:	eng
Schlagworte:	Algorithms Amino Acid Substitution Biological and medical sciences Fundamental and applied biological sciences. Psychology General aspects Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) Mutation Protein Conformation Proteins - chemistry Proteins - genetics Thermodynamics
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container_title	Bioinformatics
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creator	Huang, Liang-Tsung Gromiha, M. Michael Ho, Shinn-Ying
description	We have developed a web server, iPTREE-STAB for discriminating the stability of proteins (stabilizing or destabilizing) and predicting their stability changes (ΔΔG) upon single amino acid substitutions from amino acid sequence. The discrimination and prediction are mainly based on decision tree coupled with adaptive boosting algorithm, and classification and regression tree, respectively, using three neighboring residues of the mutant site along N- and C-terminals. Our method showed an accuracy of 82% for discriminating the stabilizing and destabilizing mutants, and a correlation of 0.70 for predicting protein stability changes upon mutations. Availability: http://bioinformatics.myweb.hinet.net/iptree.htm Contact: michael-gromiha@aist.go.jp Supplementary information: Dataset and other details are given.
doi_str_mv	10.1093/bioinformatics/btm100
format	Article
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Michael</creatorcontrib><creatorcontrib>Ho, Shinn-Ying</creatorcontrib><title>iPTREE-STAB: interpretable decision tree based method for predicting protein stability changes upon mutations</title><title>Bioinformatics</title><addtitle>Bioinformatics</addtitle><description>We have developed a web server, iPTREE-STAB for discriminating the stability of proteins (stabilizing or destabilizing) and predicting their stability changes (ΔΔG) upon single amino acid substitutions from amino acid sequence. The discrimination and prediction are mainly based on decision tree coupled with adaptive boosting algorithm, and classification and regression tree, respectively, using three neighboring residues of the mutant site along N- and C-terminals. Our method showed an accuracy of 82% for discriminating the stabilizing and destabilizing mutants, and a correlation of 0.70 for predicting protein stability changes upon mutations. 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Michael ; Ho, Shinn-Ying</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c580t-9fb44f9a558d94cbbfa2bc186aded81c9ac48035b6318269a1e1e8bdffa809a73</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2007</creationdate><topic>Algorithms</topic><topic>Amino Acid Substitution</topic><topic>Biological and medical sciences</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>General aspects</topic><topic>Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)</topic><topic>Mutation</topic><topic>Protein Conformation</topic><topic>Proteins - chemistry</topic><topic>Proteins - genetics</topic><topic>Thermodynamics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Huang, Liang-Tsung</creatorcontrib><creatorcontrib>Gromiha, M. 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subjects	Algorithms Amino Acid Substitution Biological and medical sciences Fundamental and applied biological sciences. Psychology General aspects Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) Mutation Protein Conformation Proteins - chemistry Proteins - genetics Thermodynamics
title	iPTREE-STAB: interpretable decision tree based method for predicting protein stability changes upon mutations
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