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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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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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