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.
Gront
Dominik
D
Department of Physics, Michigan Technological University, Houghton, MI 49931-1295, USA.
Kolinski
Andrzej
A
Hansmann
Ulrich H E
UH
D000465:Algorithms; D003198:Computer Simulation; D009010:Monte Carlo Method; D011487:Protein Conformation; D013696:Temperature