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Protein structure prediction by tempering spatial constraints

Journal of Computer-Aided Molecular Design volume 19, pages 603–608 (2005)Cite this article

Summary

The probability to predict correctly a protein structure can be enhanced through introduction of spatial constraints – either from NMR experiments or from homologous structures. However, the additional constraints lead often to new local energy minima and worse sampling efficiency in simulations. In this work, we present a new parallel tempering variant that alleviates the energy barriers resulting from spatial constraints and therefore yields to an enhanced sampling in structure prediction simulations.

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Acknowledgements

Support by a research grant from the National Institutes of Health (GM062838) and a grant from KBN (3 T09A 087 028) is gratefully acknowledged.

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Authors and Affiliations

  1. Department of Physics, Michigan Technological University, Houghton, MI, 49931-1295, USA

    Dominik Gront & Ulrich H.E. Hansmann

  2. Faculty of Chemistry, Warsaw University, Pasteura 1, 02-093, Warsaw, Poland

    Dominik Gront & Andrzej Kolinski

Authors
  1. Dominik Gront
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  2. Andrzej Kolinski
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  3. Ulrich H.E. Hansmann
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Correspondence to Andrzej Kolinski.

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Gront, D., Kolinski, A. & Hansmann, U.H. Protein structure prediction by tempering spatial constraints. J Comput Aided Mol Des 19, 603–608 (2005). https://doi.org/10.1007/s10822-005-9016-0

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  • DOI: https://doi.org/10.1007/s10822-005-9016-0

Key words

  • Monte Carlo sampling
  • protein structure prediction
  • replica method

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