Monte Carlo Multiple Minimum

The molecule preparation step includes also conformational expansion using a torsional search or a combined Monte Carlo Multiple Minimum/Low Mode search. During the search, the intramolecular hydrogen bonds are not considered. Molecules can be minimized, OPLS-2005 or MMFF force fields [86, 87] are available, and also two continuum solvation models (distance-dependent dielectric or GB/SA). A double criterion is used to eliminate redundant conformations it uses distances between pairs of corresponding atoms within a 1 kcal moh1 energy window. 

Conformational analysis sampling method MCMM Me (Monte Carlo Multiple Minimum)... 

Ripoll D R and H A Scheraga 1989. On the Multiple-Minimum Problem in the Conformational Anal of Polypeptides. IB. An Electrostatically Driven Monte Carlo Method Tests on met-Enkepha journal of Protein Chemistry 8 263-287. 

To overcome the limitations of the database search methods, conformational search methods were developed [95,96,109]. There are many such methods, exploiting different protein representations, objective function tenns, and optimization or enumeration algorithms. The search algorithms include the minimum perturbation method [97], molecular dynamics simulations [92,110,111], genetic algorithms [112], Monte Carlo and simulated annealing [113,114], multiple copy simultaneous search [115-117], self-consistent field optimization [118], and an enumeration based on the graph theory [119]. 

The seven compounds were first subjected to an exhaustive conformational search utilizing the Monte Carlo (MC) Multiple Minimum algorithm as available in MacroModel. The resulting conformers were then clustered using distances between the potential pharmacophore features. A minimum energy conformation in each of the clusters was used as input to DISCO algorithm. DISCO models were visually inspected and one of them was used as a 3-D query in the... 

Li Z, Scheraga HA. Monte Carlo minimization approach to the multiple-minimum problem in protein folding. Proc Natl Acad Sci USA 1987 84 6611-6615. 

One of the ways of circumventing the problem of finding multiple energy minima of complex molecules is to turn to more sophisticated techniques that are capable of sampling phase space efficiently without the need to home in on particular minimum energy conformations. The two most useful techniques are molecular dynamics (MD) and the Monte Carlo (MC) method. Both approaches make use of the same types of potential functions used in molecular mechanics, but are designed to sample conformation space such that a Boltzmann distribution of states is generated. MC and MD techniques for molecular systems have been widely reviewed [11-14], and only the basics of the two methods are described below. 

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