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An Introduction to Protein Contact Prediction

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Bioinformatics

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 453))

Abstract

A fundamental problem in molecular biology is the prediction of the three-dimensional structure of a protein from its amino acid sequence. However, molecular modeling to find the structure is at present intractable and is likely to remain so for some time, hence intermediate steps such as predicting which residues pairs are in contact have been developed. Predicted contact pairs have been used for fold prediction, as an initial condition or constraint for molecular modeling, and as a filter to rank multiple models arising from homology modeling. As contact prediction has advanced it is becoming more common for 3D structure predictors to integrate contact prediction into structure building, as this often gives information that is orthogonal to that produced by other methods. This chapter shows how evolutionary information contained in protein sequences and multiple sequence alignments can be used to predict protein structure, and the state-of-the-art predictors and their methodologies are reviewed.

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Acknowledgments

The authors gratefully acknowledge financial support from the University of Queensland, the ARC Australian Centre for Bio-informatics and the Institute for Molecular Bioscience. The first author would also like to acknowledge the support of Prof. Kevin Burrage's Australian Federation Fellowship.

Author information

Authors and Affiliations

  1. ARC Centre of Excellence in Bioinformatics, Institute for Molecular Bioscience and Advanced Computational Modelling Centre, The University of Queensland, Brisbane, Queensland, Australia

    Nicholas Hamilton

  2. School of Molecular and Microbial Sciences and Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia

    Thomas Huber

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  1. Nicholas Hamilton
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  2. Thomas Huber
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Editor information

Editors and Affiliations

  1. School of Mathematical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia

    Jonathan M. Keith PhD

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© 2008 Humana Press, a part of Springer Science+Business Media, LLC

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Hamilton, N., Huber, T. (2008). An Introduction to Protein Contact Prediction. In: Keith, J.M. (eds) Bioinformatics. Methods in Molecular Biology™, vol 453. Humana Press. https://doi.org/10.1007/978-1-60327-429-6_3

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  • DOI: https://doi.org/10.1007/978-1-60327-429-6_3

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-60327-428-9

  • Online ISBN: 978-1-60327-429-6

  • eBook Packages: Springer Protocols

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