Real-value prediction of backbone torsion angles

Proteins
Bin XueYaoqi Zhou

Abstract

The backbone structure of a protein is largely determined by the phi and psi torsion angles. Thus, knowing these angles, even if approximately, will be very useful for protein-structure prediction. However, in a previous work, a sequence-based, real-value prediction of psi angle could only achieve a mean absolute error of 54 degrees (83 degrees, 35 degrees, 33 degrees for coil, strand, and helix residues, respectively) between predicted and actual angles. Moreover, a real-value prediction of phi angle is not yet available. This article employs a neural-network based approach to improve psi prediction by taking advantage of angle periodicity and apply the new method to the prediction to phi angles. The 10-fold-cross-validated mean absolute error for the new method is 38 degrees (58 degrees, 33 degrees, 22 degrees for coil, strand, and helix, respectively) for psi and 25 degrees (35 degrees, 22 degrees, 16 degrees for coil, strand, and helix, respectively) for phi. The accuracy of real-value prediction is comparable to or more accurate than the predictions based on multistate classification of the phi-psi map. More accurate prediction of real-value angles will likely be useful for improving the accuracy of fold recognition and ab...Continue Reading

References

Jan 1, 1978·Annual Review of Biochemistry·P Y Chou, G D Fasman
Jan 1, 1968·Advances in Protein Chemistry·G N Ramachandran, V Sasisekharan
Jun 1, 1995·Protein Science : a Publication of the Protein Society·J S EvansW A Goddard
Jun 2, 1995·Journal of Molecular Biology·B H Park, M Levitt
Jan 20, 1993·Journal of Molecular Biology·H S KangB Lee
Jan 1, 1997·Folding & Design·X F de la CruzB Lee
Aug 5, 2000·Journal of Molecular Biology·C BystroffD Baker
Feb 11, 2003·Proteins·Shandar AhmadAkinori Sarai
Feb 28, 2004·Bioinformatics·Rui KuangAn-Suei Yang
Dec 21, 2004·Protein Science : a Publication of the Protein Society·Leszek Rychlewski, Daniel Fischer
Mar 22, 2005·Proteins·Matthew J Wood, Jonathan D Hirst
Dec 15, 2005·Bioinformatics·Yao-Ming Huang, Christopher Bystroff
Sep 29, 2006·Bioinformatics·Olav Zimmermann, Ulrich H E Hansmann
Oct 26, 2006·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Catherine MooneyGianluca Pollastri
Nov 1, 2006·Proceedings of the National Academy of Sciences of the United States of America·George D RoseAmos Maritan
May 31, 2007·Proceedings of the National Academy of Sciences of the United States of America·Andrea CavalliMichele Vendruscolo

❮ Previous
Next ❯

Citations

Dec 23, 2009·BMC Bioinformatics·Petros Kountouris, Jonathan D Hirst
Mar 12, 2010·Journal of the American Statistical Association·Kristin P LennoxJerry W Tsai
Apr 18, 2014·Journal of the Royal Society, Interface·Agnel Praveen Joseph, Alexandre G de Brevern
Mar 23, 2011·Theoretical Chemistry Accounts·Yaoqi ZhouHongxing Lei
Feb 6, 2016·Journal of Computational Chemistry·Md Tamjidul HoqueYaoqi Zhou
Dec 24, 2015·Journal of Computational Chemistry·Yuedong Yang, Yaoqi Zhou
Aug 29, 2014·PloS One·Harinder SinghGajendra P S Raghava
Sep 20, 2017·BMC Bioinformatics·Haiou LiJianlin Cheng
Feb 6, 2019·BMC Bioinformatics·Hamendra Manhar ReddyTatushiko Tsunoda
Jan 4, 2017·Briefings in Bioinformatics·Yuedong YangYaoqi Zhou
Nov 12, 2020·Scientific Reports·Fereshteh MataeimoghadamAbdul Sattar
Sep 4, 2008·Journal of Chemical Information and Modeling·Olav Zimmermann, Ulrich H E Hansmann

❮ 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.