2006
DOI: 10.1021/jp060365r
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Hydrophobic Aided Replica Exchange:  an Efficient Algorithm for Protein Folding in Explicit Solvent

Abstract: A hydrophobic aided replica exchange method (HAREM) is introduced to accelerate the simulation of allatom protein folding in explicit solvent. This method is based on exaggerating the hydrophobic effect of various protein amino acids in water by attenuating the protein-water attractive interactions (mimicking the Chaperon effect) while leaving other interactions among protein atoms and water molecules unchanged. The method is applied to a small representative protein, the R-helix 3K(I), and it is found that th… Show more

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Cited by 75 publications
(53 citation statements)
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“…Generalized ensemble (GE) algorithms, such as the replica exchange method (REM), or parallel tempering (1,2) and simulated tempering (ST) (3,4), are popular approaches for studying biomolecular folding (5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15). They attempt to overcome the sampling problem by inducing a random walk in temperature space while maintaining canonical sampling at each temperature.…”
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confidence: 99%
“…Generalized ensemble (GE) algorithms, such as the replica exchange method (REM), or parallel tempering (1,2) and simulated tempering (ST) (3,4), are popular approaches for studying biomolecular folding (5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15). They attempt to overcome the sampling problem by inducing a random walk in temperature space while maintaining canonical sampling at each temperature.…”
mentioning
confidence: 99%
“…With the growing popularity of replica exchange, particularly for the simulation of biomolecules (5), the overlap problem has received increasing attention. Strategies proposed to address this problem include tempering or perturbing only a subset of degrees of freedom (6)(7)(8); and the use of Tsallis-like (9-11), multicanonical (12)(13)(14), or expanded-ensemble (15, 16) probability distributions.…”
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confidence: 99%
“…Another advantage of the method is that it does not require that the potential separate into different parts, like solvent/solute 21,22 or hydrophobic/hydrophilic. 2 The method can be applied to arbitrary systems, but it is flexible enough that the system can be separated into scaled and unscaled parts if that is advantageous ͓see Eq.…”
Section: Discussionmentioning
confidence: 99%
“…Prior Hamiltonian RE applications have all been constant volume. 2,14,[19][20][21][22] Hamiltonian RE will change the virial contribution to the pressure and so the volume will be different from that of the original Hamiltonian. The REDS method gets around this by a suitable scaling of the pressure.…”
Section: ͑12͒mentioning
confidence: 99%
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