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Rapid and Accurate Protein Side Chain Prediction with Local Backbone Information

  • Conference paper
Research in Computational Molecular Biology (RECOMB 2008)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 4955))

Abstract

High-accuracy protein structure modeling demands accurate and very fast side chain prediction since such a procedure must be repeatedly called at each step of structure refinement. Many known side chain prediction programs, such as SCWRL and TreePack, depend on the philosophy that global information and pairwise energy function must be used to achieve high accuracy. These programs are too slow to be used in the case when side chain packing has to be used thousands of times, such as protein structure refinement and protein design.

We present an unexpected study that local backbone information can determine side chain conformations accurately. LocalPack, our side chain packing program which is based on only local information, achieves equal accuracy as SCWRL and TreePack, yet runs 4-14 times faster, hence providing a key missing piece in our efforts to high-accuracy protein structure modeling.

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Authors and Affiliations

  1. David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, Ontario, Canada, N2L 6P7

    Jing Zhang, Xin Gao & Ming Li

  2. The Institute for Theoretical Computer Science, Department of Computer Science and Technology, Tsinghua University, Beijing, 100084, China

    Jing Zhang

  3. Toyota Technological Institute at Chicago, Chicago, IL, USA, 60637

    Jinbo Xu

Authors
  1. Jing Zhang
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  2. Xin Gao
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  3. Jinbo Xu
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  4. Ming Li
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Martin Vingron Limsoon Wong

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Zhang, J., Gao, X., Xu, J., Li, M. (2008). Rapid and Accurate Protein Side Chain Prediction with Local Backbone Information. In: Vingron, M., Wong, L. (eds) Research in Computational Molecular Biology. RECOMB 2008. Lecture Notes in Computer Science(), vol 4955. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-78839-3_25

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  • DOI: https://doi.org/10.1007/978-3-540-78839-3_25

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-78838-6

  • Online ISBN: 978-3-540-78839-3

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