Monte Carlo minimization

Q and H A Scheraga 1987. Monte-Carlo-minimization Approach to the Multiple-minima Problem... 

Li Z Q and H A Scheraga 1987. Monte Carlo Minimization Approach to the Multiple Minima Problem, in Protein Folding. Proceedings of the National Academy of Sciences USA 84 6611-6615. 

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

Trosset J-Y, Scheraga HA (1999) Flexible docking simulations scaled collective variable Monte Carlo minimization approach using Bezier splines, and comparison with a standard Monte Carlo algorithm. J Comp Chem 20 244-252... 

In order to find the relevant conformers, the authors employed a Monte Carlo/minimization strategy that is described in more detail in the next chapter - in practice, (2/ , 4S )-l-hydroxy-2,4-dimethylhex-5-ene is sufficiently small that one could survey every possible torsional isomer by brute force, but it would be very tedious. Table 2.2 shows, for the nine lowest energy conformers, their predicted energies, their contribution to the 300 K equilibrium population, their individual 1 Jcc coupling constants between atoms C(2)C(5), C(2)C(8), C( 1 )C(4), and C(4)C(7), and the mean absolute error in these coupling... 

Simulations Scaled Collective Variable Monte Carlo Minimization Approach Using Bezier Splines, and Comparison with a Standard Monte Carlo Algorithm. 

Finally, dynamic structure-based pharmacophore models can be derived through a method first described by Carlson et al that uses multiple conformations of the target protein, which are obtained either by molecular dynamics simulation or by the use of multiple experimentally determined conformations. The binding sites of the respective snapshots are flooded with small molecular probes (e.g., methanol for hydrogen-bond interactions and benzene for aromatic hydrophobic interactions) and while the protein structure is held rigid the probe molecules are subjected to a low-temperature Monte Carlo minimization where they undergo multiple, simultaneous gas-phase... 

In Monte Carlo minimization, an additional step is inserted after the random walk before Metropolis evaluation. This step is a... 

ROSETTA DOCK works by simultaneous optimization of side-chain conformation and rigid-body position of the two docking partners. The former is performed by a packing algorithm and the latter is performed by a rigid-body Monte Carlo minimization strategy... 

Sale K, Sar C, Sharp KA, Hideg K, Fajer PG (2002) Structural determination of spin label immobilization and orientation a Monte Carlo minimization approach. J Magn Reson 156 104-112... 

M. Visquez, E. Meirovitch, and H. Meirovitch,/. Phys. Chem., 98,9380 (1994). A Free Energy Based Monte Carlo Minimization Procedure for Macromolecules. 

Caflisch et al. demonstrated that a two-step procedure incorporating a Monte Carlo minimization procedure can dock flexible oligopeptides to static proteins. Step one involves rigid rotations and translations of a preselected conformation. Step two involves taking the low energy conformation(s) produced in step one and carrying out 400 cycles of Monte Carlo minimization. The bound conformation of the HIV protease inhibitor MVT-101 was well reproduced by the method. 

A second approach incorporates free energy information into the branch and bound algorithm. Specifically, harmonic entropic contributions are calculated and included at each minima of the upper and lower bounding functions. In this way, the progression of lower and upper bounds includes a temperature-dependent entropic term. A similar modification to the Monte Carlo minimization method has also been proposed [87] and has been shown to be effective in locating low-energy conformers of peptides [88,89]. 

H. Meirovitch and E. Meirovitch, Efficiency of monte carlo minimization procedures and their use in analysis of nmr data obtained from flexible peptides. J. Comput. Chem. 18, 240-253 (1997). 

H. Meirovitch and M. Vasquez, Efficiency of simulated annealing and the monte carlo minimization method for generating a set of low energy structures of peptides. J. MoL Struct. (Theochem.) 398-399, 517-522 (1997). 

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