Monte-Carlo with minimization

A. Nayeem, J. Vila, and H. A. Scheraga. A comparative study of the simulated-annealing and monte carlo-with-minimization approaches to the minimum-energy structures of polypeptides [met]-enkephalin. J. Comp. Chem., 12(5) 594-605, 1991. 

Simulated annealing, ESMC [108,109,161], Monte Carlo with minimization [162], genetic algorithms [64,163-165], and the combination of genetic algorithms with Monte Carlo sampling have been successfully used in the past to find the near-native conformations of reduced models of small proteins [68]. 

Nanias M et al (2005) Protein structure prediction with the UNRES fOTce-field using replica-exchange Monte Carlo-with-minimization comparison with MCM, CSA, and CFMC. J Comput Chem 26 1472-1486... 

As stated above, the most important missing piece in protein folding theory is an accurate all-atom potential. Recently there has been much effort in this direction, and much more is needed [48,55,72-77]. The existence of a potential satisfying minimal criteria such as folding and stability for a single protein was demonstrated in [73]. It is not a realistic potential by any means, but its existence validates the all-atom, implicit solvent, Monte Carlo approach as a serious candidate for theory. The method used to derive this potential was ad hoc, and has recently been compared with other standard methods in a rigorous and illuminating study [77]. 

Monte Carlo simulations and energy minimization procedures of the non-bonding interactions between rigid molecules and fixed zeolite framework provide a reasonable structural picture of DPP occluded in acidic ZSM-5. Molecular simulations carried out for DPB provide evidence of DPB sorption into the void space of zeolites and the preferred locations lay in straight channels in the vicinity of the intersection with the zigzag channel in interaction with H+ cation (figure 1). 

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