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Protein Secondary Structure Assignments and Their Usefulness for Dihedral Angle Prediction

  • Eshel FaraggiEmail author
  • Andrzej Kloczkowski
Chapter
Part of the Springer Series on Bio- and Neurosystems book series (SSBN, volume 8)

Abstract

We present and compare different protein secondary structure assignment methods and the effect of their use in dihedral angle prediction. It is found that consensus reassignment of secondary structure tends to improve the accuracy of secondary structure prediction. However, it is less useful for the prediction of the dihedral angles than a better defined reassignment method based on angle values. Considering reassigned residues, we find them to be hard to predict. We find the most significant improvement for reassigned residues is due to our new reassignment method. This method also reassigns a smaller number of residues as compared to consensus methods. We additionally find that improvements to the accuracy of dihedral angle prediction is due both to single residue and local-neighborhood effects.

Keywords

Dihedral angle prediction Secondary structure prediction Secondary structure assignment Protein structure Machine learning 

Notes

Acknowledgements

We gratefully acknowledge support from National Science Foundation grant DBI 1661391, and Bridge funds provided by The Research Institute at Nationwide Children’s Hospital.

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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  1. 1.Department of PhysicsIndiana University Purdue University IndianapolisIndianapolisUSA
  2. 2.Department of PhysicsButler UniversityIndianapolisUSA
  3. 3.Battelle Center for Mathematical MedicineThe Research Institute at Nationwide Children’s HospitalColumbusUSA
  4. 4.Physics Division, Research and Information SystemsLLCIndianapolisUSA
  5. 5.Department of PediatricsThe Ohio State UniversityColumbusUSA

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