Parallel Tempering in Rosetta Practice
نویسندگان
چکیده
Parallel Tempering (PT) is an effective algorithm to overcome the slow convergence in low-temperature protein simulation by initiating multiple systems to run at multiple temperature levels and randomly switch with neighbor temperature levels. We implemented the PT scheme in the Rosetta to explore the rough energy landscape in protein folding and to improve the success rate of Rosetta in topologically complex structures. Compared to the original Simulated Annealing (SA) scheme in Rosetta, our preliminary computational results show that the PT scheme in Rosetta program exhibits a wider range sampling in the potential energy surface in protein folding.
منابع مشابه
Extensive exploration of conformational space improves Rosetta results for short protein domains.
With some simplifications, computational protein folding can be understood as an optimization problem of a potential energy function on a variable space consisting of all conformation for a given protein molecule. It is well known that realistic energy potentials are very "rough" functions, when expressed in the standard variables, and the folding trajectories can be easily trapped in multiple ...
متن کاملar X iv : p hy si cs / 0 50 81 11 v 2 1 9 A ug 2 00 5 Parallel Tempering : Theory , Applications , and New Perspectives
We review the history of the parallel tempering simulation method. From its origins in data analysis, the parallel tempering method has become a standard workhorse of physiochemical simulations. We discuss the theory behind the method and its various generalizations. We mention a selected set of the many applications that have become possible with the introduction of parallel tempering and we s...
متن کاملDetermination of normalizing constants for simulated tempering
In this paper, we propose to estimate the normalizing constants for simulated tempering by a modified histogram algorithm, the so-called contour Monte Carlo algorithm, and compare the efficiency of simulated tempering and parallel tempering. Our analysis reveals that simulated tempering tends to mix faster than parallel tempering at low temperature levels for simulating from complex systems. Th...
متن کامل. co m p - ph ] 1 7 A ug 2 00 5 Parallel Tempering : Theory , Applications , and New Perspectives
We review the history of the parallel tempering simulation method. From its origins in data analysis, the parallel tempering method has become a standard workhorse of physiochemical simulations. We discuss the theory behind the method and its various generalizations. We mention a selected set of the many applications that have become possible with the introduction of parallel tempering and we s...
متن کامل. co m p - ph ] 1 9 A ug 2 00 5 Parallel Tempering : Theory , Applications , and New Perspectives
We review the history of the parallel tempering simulation method. From its origins in data analysis, the parallel tempering method has become a standard workhorse of physiochemical simulations. We discuss the theory behind the method and its various generalizations. We mention a selected set of the many applications that have become possible with the introduction of parallel tempering and we s...
متن کامل