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DOCK/PIERR: Web Server for Structure Prediction of Protein–Protein Complexes

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Protein Structure Prediction

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1137))

Abstract

In protein docking we aim to find the structure of the complex formed when two proteins interact. Protein–protein interactions are crucial for cell function. Here we discuss the usage of DOCK/PIERR. In DOCK/PIERR, a uniformly discrete sampling of orientations of one protein with respect to the other, are scored, followed by clustering, refinement, and reranking of structures. The novelty of this method lies in the scoring functions used. These are obtained by examining hundreds of millions of correctly and incorrectly docked structures, using an algorithm based on mathematical programming, with provable convergence properties.

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Acknowledgements

The authors acknowledge funding from NIH grant GM59796 and Welch grant F-1783.

Author information

Authors and Affiliations

  1. Department of Computer Science, University of Texas at Austin, Austin, TX, USA

    Shruthi Viswanath

  2. Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, TX, USA

    Shruthi Viswanath

  3. WalmartLabs, San Bruno, CA, USA

    D. V. S. Ravikant

  4. Department of Chemistry and Biochemistry and Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, TX, USA

    Ron Elber

Authors
  1. Shruthi Viswanath
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  2. D. V. S. Ravikant
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  3. Ron Elber
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Editor information

Editors and Affiliations

  1. Purdue University Dept. Biological Science, West Lafayette, Indiana, USA

    Daisuke Kihara

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Viswanath, S., Ravikant, D.V.S., Elber, R. (2014). DOCK/PIERR: Web Server for Structure Prediction of Protein–Protein Complexes. In: Kihara, D. (eds) Protein Structure Prediction. Methods in Molecular Biology, vol 1137. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-0366-5_14

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  • DOI: https://doi.org/10.1007/978-1-4939-0366-5_14

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-0365-8

  • Online ISBN: 978-1-4939-0366-5

  • eBook Packages: Springer Protocols

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