Protein structure prediction by tempering spatial constraints
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 wordsMonte Carlo sampling protein structure prediction replica method
Unable to display preview. Download preview PDF.
Support by a research grant from the National Institutes of Health (GM062838) and a grant from KBN (3 T09A 087 028) is gratefully acknowledged.
- 2.Hansmann U.H.E. (2004). In: Wille L.T.(ed). New Directions in Statistical Physics - Econophysics, Bioinformatics and Pattern Recognition. Springer Verlag, Berlin, pp.173Google Scholar
- 3.Hukushima, K. and Nemoto, K., J. Phys. Soc. Jpn., 65 (1996) 1604. Geyer, G.J., Stat. Sci., 7 (1992) 437Google Scholar
- 6.Kolinski A. (2004). Acta. Biochim. Pol. 51:349Google Scholar