Prediction of cis/trans isomerization in proteins using PSI-BLAST profiles and secondary structure information

BMC Bioinformatics
Jiangning SongThomas Huber

Abstract

The majority of peptide bonds in proteins are found to occur in the trans conformation. However, for proline residues, a considerable fraction of Prolyl peptide bonds adopt the cis form. Proline cis/trans isomerization is known to play a critical role in protein folding, splicing, cell signaling and transmembrane active transport. Accurate prediction of proline cis/trans isomerization in proteins would have many important applications towards the understanding of protein structure and function. In this paper, we propose a new approach to predict the proline cis/trans isomerization in proteins using support vector machine (SVM). The preliminary results indicated that using Radial Basis Function (RBF) kernels could lead to better prediction performance than that of polynomial and linear kernel functions. We used single sequence information of different local window sizes, amino acid compositions of different local sequences, multiple sequence alignment obtained from PSI-BLAST and the secondary structure information predicted by PSIPRED. We explored these different sequence encoding schemes in order to investigate their effects on the prediction performance. The training and testing of this approach was performed on a newly enlarg...Continue Reading

References

Oct 20, 1975·Biochimica Et Biophysica Acta·B W Matthews
Apr 1, 1991·Medical Decision Making : an International Journal of the Society for Medical Decision Making·R M Centor
Oct 1, 1990·Biochimie·J Janin
Jul 5, 1990·Journal of Molecular Biology·D E StewartJ E Wampler
Jan 1, 1993·Advances in Protein Chemistry·F X SchmidE R Schönbrunner
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Jun 27, 1998·Journal of Molecular Biology·U ReimerG Fischer
Aug 12, 1998·Nature Structural Biology·M S WeissR Hilgenfeld
Feb 5, 1999·Journal of Molecular Biology·A JabsR Hilgenfeld
Jan 5, 2000·Proceedings of the National Academy of Sciences of the United States of America·M P BrownD Haussler
Dec 12, 2002·Biochemistry·William J WedemeyerHarold A Scheraga
Jul 10, 2003·Chemical Reviews·Christophe Dugave, Luc Demange
Aug 13, 2003·Bioinformatics·Guoli Wang, Roland L Dunbrack
Feb 27, 2004·The Journal of Peptide Research : Official Journal of the American Peptide Society·M-L WangW-B Xu
Apr 10, 2004·Bioinformatics·Eibe FrankIan H Witten
Sep 24, 2004·Biophysical Chemistry·Young Kee Kang, Ha Young Choi
Dec 21, 2004·Proteins·Stephan LorenzenCornelius Frömmel
Dec 23, 2004·Bioinformatics·James R Bradford, David R Westhead
Jan 13, 2005·Proteins·Zheng YuanRohan D Teasdale
Feb 22, 2005·BMC Bioinformatics·Shandar Ahmad, Akinori Sarai
Mar 31, 2005·Bioinformatics·Qidong ZhangWilliam J Welsh
Jun 7, 2005·Nature Structural & Molecular Biology·Barbara EckertFranz X Schmid
Sep 20, 2005·Proteins·Yu-Ching Chen, Jenn-Kang Hwang
May 10, 2011·Molecular Neurobiology·Melanie GerardVeerle Baekelandt

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Citations

Jul 27, 2010·Interdisciplinary Sciences, Computational Life Sciences·Xuan-Min GuangMeng-Long Li
May 10, 2008·Bioinformatics·Jiangning SongTatsuya Akutsu
Feb 5, 2010·Bioinformatics·Jiangning SongJames C Whisstock
Feb 18, 2011·Journal of Bioinformatics and Computational Biology·Jiangning SongRobert N Pike
Oct 4, 2006·BMC Bioinformatics·Jiangning Song, Kevin Burrage
Dec 22, 2010·BMC Genomics·Lawrence J K WeeJoo Chuan Tong
Apr 11, 2012·International Journal of Molecular Sciences·Xiaowei ZhaoMinghao Yin
Jun 4, 2013·Amino Acids·Pierrick CraveurJoseph Rebehmed
Sep 12, 2015·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Dong-Jun YuHong-Bin Shen
Mar 17, 2015·Nature Structural & Molecular Biology·Jonas NoeskeJamie H D Cate
Jun 3, 2017·PloS One·Sabri BoughorbelMohammed El-Anbari
Jun 22, 2017·Journal of Proteome Research·Sreetama DasDebnath Pal
Feb 26, 2009·Proteins·Aurélie BornotAlexandre G de Brevern
Aug 8, 2019·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Jack HansonYaoqi Zhou
May 22, 2009·Journal of Neurochemistry·Isabelle M PaulsenSusan M J Dunn
Jan 4, 2017·Briefings in Bioinformatics·Yuedong YangYaoqi Zhou
Aug 8, 2015·Acta Crystallographica. Section D, Biological Crystallography·Wouter G TouwGert Vriend
Apr 25, 2018·Journal of Molecular Recognition : JMR·Rahul MishraHelen Blanchard
Apr 9, 2020·Journal of the American Chemical Society·Annika UrbanekPau Bernadó
Aug 18, 2018·Journal of Chemical Information and Modeling·Jaswinder SinghYaoqi Zhou
Sep 30, 2009·Insect Biochemistry and Molecular Biology·Susan E BrownPeter D East

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Methods Mentioned

BETA
protein folding
X-ray

Software Mentioned

TransPep
blastpgp
MathType
PSIPRED
CISPEPpred
CisPep
PSICES
Weka
SVM
Weka package

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