Chapter 3. Automated Prediction of Protein Function from Sequence

  1. Janusz M. Bujnicki4,5
  1. Meghana Chitale1,
  2. Troy Hawkins2,
  3. Daisuke Kihara3

Published Online: 18 DEC 2008

DOI: 10.1002/9780470741894.ch3

Book Title

Prediction of Protein Structures, Functions, and Interactions

Prediction of Protein Structures, Functions, and Interactions

Additional Information

How to Cite

Chitale, M., Hawkins, T. and Kihara, D. (2008) Automated Prediction of Protein Function from Sequence, in Prediction of Protein Structures, Functions, and Interactions (ed J. M. Bujnicki), John Wiley & Sons, Ltd, Chichester, UK. doi: 10.1002/9780470741894.ch3

Editor Information

  1. 4

    Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland

  2. 5

    Laboratory of Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, 61-614 Poznan, Poland

Author Information

  1. 1

    Department of Computer Science, College of Science, Purdue University, West Lafayette, IN, 47907, USA

  2. 2

    Department of Biological Sciences, College of Science, Purdue University, West Lafayette, IN, 47907, USA

  3. 3

    Department of Biological Sciences/Computer Science, Markey Center for Structural Biology, College of Science, Purdue University, West Lafayette, IN, 47907, USA

Publication History

  1. Published Online: 18 DEC 2008
  2. Published Print: 19 DEC 2008

ISBN Information

Print ISBN: 9780470517673

Online ISBN: 9780470741894

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CHAPTER TOOLS

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Keywords:

  • computational techniques and sequence gene function prediction;
  • genes and sequence similarity;
  • homology search methods;
  • sequence-based protein function prediction strategy;
  • PSI-BLAST - profile-to-sequence comparisons;
  • automated GO term prediction methods;
  • protein function prediction (PFP) algorithm;
  • sequence-based function prediction and gene genomic context

Summary

This chapter contains sections titled:

  • Introduction

  • Principle of Inferring Function from Sequence Similarity

  • Homology Search Methods

  • Predicting Function from the Other Types of Information

  • Limitations and Problems of Function Prediction from Sequence

  • Controlled Vocabularies for Gene Function Annotation

  • Gene Ontology

  • Other Functional Ontologies

  • Quantifying Functional Similarity

  • Automated GO Term Prediction Methods

  • Protein Function Prediction (PFP) Algorithm

  • PFP Benchmark Results

  • Comparative Genomics Based Methods

  • Subcellular Localization Prediction

  • Identification of Functionally Important Residues

  • Function Prediction Competitions

  • Summary

  • Acknowledgement

  • References

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