7. Contact Map Prediction by Machine Learning

  1. Huzefa Rangwala3 and
  2. George Karypis4
  1. Alberto J.M. Martin1,
  2. Catherine Mooney1,
  3. Ian Walsh2 and
  4. Gianluca Pollastri2

Published Online: 7 SEP 2010

DOI: 10.1002/9780470882207.ch7

Introduction to Protein Structure Prediction: Methods and Algorithms

Introduction to Protein Structure Prediction: Methods and Algorithms

How to Cite

Martin, A. J.M., Mooney, C., Walsh, I. and Pollastri, G. (2010) Contact Map Prediction by Machine Learning, in Introduction to Protein Structure Prediction: Methods and Algorithms (eds H. Rangwala and G. Karypis), John Wiley & Sons, Inc., Hoboken, NJ, USA. doi: 10.1002/9780470882207.ch7

Editor Information

  1. 3

    Department of Computer Science, George Mason University, Fairfax, VA 22030, USA

  2. 4

    Department of Computer Science, University of Minnesota Minneapolis, MN 55455, USA

Author Information

  1. 1

    Shields Lab, School of Medicine and Medical Science, University College Dublin, Ireland

  2. 2

    Complex and Adaptive Systems Lab, School of Computer Science and Informatics, UCD Dublin, Ireland

Publication History

  1. Published Online: 7 SEP 2010
  2. Published Print: 12 NOV 2010

Book Series:

  1. Wiley Series on Bioinformatics: Computational Techniques and Engineering

Book Series Editors:

  1. Yi Pan and
  2. Albert Zomaya

ISBN Information

Print ISBN: 9780470470596

Online ISBN: 9780470882207

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Keywords:

  • contact map prediction by machine learning;
  • predicting binary contact maps, two stages - contact density prediction from primary sequence and contact map reconstruction;
  • filtering contact maps, filtering stage (NN-Filter) - correcting nonphysical contact predictions by training ensembles of artificial neural networks

Summary

This chapter contains sections titled:

  • Introduction

  • Binary Contact Map Prediction by 2 D-RNN

  • Incorporating Template Information

  • Filtering Contact Maps

  • Multi-Class Distance Maps

  • CASP 8 Evaluation

  • Conclusions

  • References