Journal of Computer-Aided Molecular Design

, Volume 19, Issue 8, pp 603–608 | Cite as

Protein structure prediction by tempering spatial constraints

  • Dominik Gront
  • Andrzej Kolinski
  • Ulrich H.E. Hansmann
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.

Key words

Monte Carlo sampling protein structure prediction replica method 

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Notes

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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Copyright information

© Springer Science+Business Media, Inc. 2005

Authors and Affiliations

  • Dominik Gront
    • 1
    • 2
  • Andrzej Kolinski
    • 2
  • Ulrich H.E. Hansmann
    • 1
  1. 1.Department of PhysicsMichigan Technological UniversityHoughtonUSA
  2. 2.Faculty of ChemistryWarsaw UniversityWarsawPoland

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