Predicting continuous local structure and the effect of its substitution for secondary structure in fragment-free protein structure prediction.

Structure
Eshel FaraggiYaoqi Zhou

Abstract

Local structures predicted from protein sequences are used extensively in every aspect of modeling and prediction of protein structure and function. For more than 50 years, they have been predicted at a low-resolution coarse-grained level (e.g., three-state secondary structure). Here, we combine a two-state classifier with real-value predictor to predict local structure in continuous representation by backbone torsion angles. The accuracy of the angles predicted by this approach is close to that derived from NMR chemical shifts. Their substitution for predicted secondary structure as restraints for ab initio structure prediction doubles the success rate. This result demonstrates the potential of predicted local structure for fragment-free tertiary-structure prediction. It further implies potentially significant benefits from using predicted real-valued torsion angles as a replacement for or supplement to the secondary-structure prediction tools used almost exclusively in many computational methods ranging from sequence alignment to function prediction.

References

Jan 20, 1993·Journal of Molecular Biology·H S KangB Lee
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Sep 24, 1999·Protein Science : a Publication of the Protein Society·M YoungS Highsmith
Sep 12, 2001·Journal of Structural Biology·B Rost
Feb 7, 2003·Proceedings of the National Academy of Sciences of the United States of America·Marian NaniasHarold A Scheraga
Aug 13, 2003·Bioinformatics·Guoli Wang, Roland L Dunbrack
Aug 20, 2003·Proceedings of the National Academy of Sciences of the United States of America·Boris Fain, Michael Levitt
Feb 28, 2004·Bioinformatics·Rui KuangAn-Suei Yang
May 6, 2004·Proceedings of the National Academy of Sciences of the United States of America·Yang Zhang, Jeffrey Skolnick
Dec 21, 2004·Briefings in Bioinformatics·Zheng Rong Yang
Jan 13, 2005·Proteins·Zheng YuanRohan D Teasdale
Jul 1, 2005·Protein Science : a Publication of the Protein Society·Daisuke Kihara
Aug 5, 2005·Proteins·Avner Schlessinger, Burkhard Rost
Sep 17, 2005·Science·Philip BradleyDavid Baker
Oct 28, 2005·Proceedings of the National Academy of Sciences of the United States of America·Haipeng GongGeorge D Rose
Dec 15, 2005·Bioinformatics·Yao-Ming Huang, Christopher Bystroff
Dec 27, 2005·The Journal of Chemical Physics·Marcos R Betancourt
Apr 7, 2006·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Yan LiuVanathi Gopalakrishnan
Jul 21, 2006·Proteins·François FerronDavid Karlin
Oct 3, 2006·Cell Biochemistry and Biophysics·Yaoqi ZhouSong Liu
Dec 13, 2006·Biophysical Journal·Predrag RadivojacA Keith Dunker
Apr 14, 2007·Current Protein & Peptide Science·Jean M BourhisSonia Longhi
Apr 14, 2007·Current Protein & Peptide Science·Zsuzsanna DosztányiIstván Simon
May 31, 2007·Proceedings of the National Academy of Sciences of the United States of America·Andrea CavalliMichele Vendruscolo
Jul 6, 2007·Cellular and Molecular Life Sciences : CMLS·A GodzikI Friedberg
Jul 11, 2007·Proceedings of the National Academy of Sciences of the United States of America·S Banu OzkanKen A Dill
Jul 27, 2007·Proteins·Gonzalo LópezAlfonso Valencia
Jul 28, 2007·Protein Science : a Publication of the Protein Society·Haipeng GongGeorge D Rose
Aug 29, 2007·PLoS Computational Biology·Anna LobleyDavid T Jones
Jan 25, 2008·Proteins·Bin XueYaoqi Zhou
Mar 11, 2008·Proceedings of the National Academy of Sciences of the United States of America·Yang ShenAd Bax
Apr 17, 2008·Proteins·Feng ZhaoJinbo Xu

❮ Previous
Next ❯

Citations

Feb 28, 2014·Journal of Chemical Information and Modeling·Ashraf Yaseen, Yaohang Li
Mar 5, 2013·Annual Review of Biophysics·Zhixiu LiYaoqi Zhou
Jan 3, 2012·Journal of Biomolecular Structure & Dynamics·Tuo ZhangYaoqi Zhou
Jan 22, 2011·Briefings in Bioinformatics·Hua ZhangLukasz Kurgan
Aug 29, 2012·Briefings in Bioinformatics·Mehdi MaadooliatJianhua Z Huang
Mar 23, 2011·Theoretical Chemistry Accounts·Yaoqi ZhouHongxing Lei
Feb 6, 2016·Journal of Computational Chemistry·Md Tamjidul HoqueYaoqi Zhou
Feb 2, 2012·Progress in Nuclear Magnetic Resonance Spectroscopy·Jakob T NielsenNiels Chr Nielsen
Dec 24, 2015·Journal of Computational Chemistry·Yuedong Yang, Yaoqi Zhou
Jun 4, 2013·Journal of Computational Chemistry·Priyanka Dhingra, Bhyravabhotla Jayaram
Sep 20, 2011·Proteins·Bohdan MonastyrskyyAndriy Kryshtafovych
Mar 27, 2015·Journal of Computer-aided Molecular Design·Barbara KalinowskaIrena Roterman
Jan 10, 2013·Journal of Biomolecular Structure & Dynamics·Jing YanLukasz Kurgan
Dec 10, 2013·Biophysical Journal·Jihua WangYaoqi Zhou
Apr 27, 2016·Nucleic Acids Research·Sheng WangJinbo Xu
Aug 29, 2014·PloS One·Harinder SinghGajendra P S Raghava
Apr 23, 2015·PloS One·Saulo H P de OliveiraCharlotte M Deane
Mar 9, 2017·Journal of Computational Chemistry·Garrett B GohAbhinav Vishnu
Nov 15, 2017·Bioinformatics·Saulo H P de OliveiraCharlotte M Deane
Aug 12, 2018·Protein Science : a Publication of the Protein Society·Tianqi MaJianpeng Ma
Jan 6, 2009·Chemistry : a European Journal·Christian TorborgMatthias Beller
Aug 30, 2011·Molecular BioSystems·Xin DengJianlin Cheng
Mar 2, 2018·Current Drug Discovery Technologies·Elaheh Kashani-AminAzadeh Ebrahim-Habibi
Aug 15, 2019·Chemistry : a European Journal·Isabel FuentesFrancesc Teixidor
Sep 20, 2017·BMC Bioinformatics·Haiou LiJianlin Cheng
May 18, 2016·The Journal of Biological Chemistry·Kh Shamsur RahmanBernhard Kaltenboeck
Aug 24, 2018·The Journal of Chemical Physics·Tianwu ZangJianpeng Ma

❮ Previous
Next ❯

Related Concepts

Related Feeds

Cajal Bodies & Gems

Cajal bodies or coiled bodies are dense foci of coilin protein. Gemini of Cajal bodies, or gems, are microscopically similar to Cajal bodies. It is believed that Cajal bodies play important roles in RNA processing while gems assist the Cajal bodies. Find the latest research on Cajal bodies and gems here.