Simulated annealing application

Briinger A, Karpins M, Petsko GA. Crystallographic refinement by simulated annealing application to crambin. Acta Crystallogr, Sect A 1989 A45 50-61. 

Brunger AT (1988) Crystallographic refinement by simulated annealing. Application to a 2.8 A resolution structure of aspartate aminotransferase. J Mol Biol 203(3) 803-816... 

W. B. Dolan, P. T. Cummings, and M. D. LeVan. Process optimization via simulated annealing application to network design. AIChE J., 35 725,1989. 

A. T. Brunger, J. Mol. Biol., 203, 803 (1988). Crystallographic Refinement by Simulated Annealing. Application to a 2.8 A Resolution Structure of Aspartate Aminotransferase. 

Sprik, M. and Klein, M.L. (1988) Optimization ofa Distributed Gaussian Basis Set using Simulated Annealing Application to the Adiabatic Dynamics of the Solvated Electron,. /. Chem. Phys. 89, 1592—1607. 

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C. Koulamas, K.R. Davis, F. Turner III, A survey of simulated annealing applications to operations research problems. Omega, 22 (1994) 41. 

Crystallographic Refinement by Simulated Annealing Application to Crambin. 

Other methods which are applied to conformational analysis and to generating multiple conformations and which can be regarded as random or stochastic techniques, since they explore the conformational space in a non-deterministic fashion, arc genetic algorithms (GA) [137, 1381 simulation methods, such as molecular dynamics (MD) and Monte Carlo (MC) simulations 1139], as well as simulated annealing [140], All of those approaches and their application to generate ensembles of conformations arc discussed in Chapter II, Section 7.2 in the Handbook. 

A particularly important application of molecular dynamics, often in conjunction with the simulated annealing method, is in the refinement of X-ray and NMR data to determine the three-dimensional structures of large biological molecules such as proteins. The aim of such refinement is to determine the conformation (or conformations) that best explain the experimental data. A modified form of molecular dynamics called restrained moleculai dynarrdcs is usually used in which additional terms, called penalty functions, are added tc the potential energy function. These extra terms have the effect of penalising conformations... 

Roitberg, A. Elber, R., Modeling side chains in peptides and proteins application of the locally enhanced sampling technique and the simulated annealing methods to find minimum energy conformations, J. Chem. Phys. 1991, 95, 9277-9287... 

Athier, G. P. Roquet L. Pibouleau et al. Process Optimization by Simulated Annealing and NLP Procedures. Application to Heat Exchanger Network Synthesis. Comput Chem Eng 21 (Suppl) S475-S480 (1997). 

This criterion requires a search through a nonconvex multidimensional conformation space that contains an immense number of minima. Optimization techniques that have been applied to the problem include Monte Carlo methods, simulated annealing, genetic methods, and stochastic search, among others. For reviews of the application of various optimization methods refer to Pardalos et al. (1996), Vasquez et al. (1994), or Schlick et al. (1999). 

The receptor relevance of BCUT descriptors has inspired several groups to apply them in conjunction with other methods. Beno and Mason reported the use of simulated annealing to optimize library design using BCUT chemistry space and four-point pharmacophores concurrently (33) and the use of chemistry spaces in conjunction with property profiles (52). The application of such composite methods to target class library design is readily apparent. Pirard and Pickett reported the application of the chemometric method, partial least squares discriminant analysis, with BCUT descriptors to successfully classify ATP-site-directed kinase inhibitors active against five different protein kinases... 

The methods of simulated annealing (26), genetic algorithms (27), and taboo search (29) are three of the most popular stochastic optimization techniques, inspired by ideas from statistical mechanics, theory of evolutionary biology, and operations research, respectively. They are applicable to our current problem and have been used by researchers for computational library design. Because SA is employed in this chapter, a more-detailed description of the (generalized) SA is given below. 

Nilges, M., Gronenborn, A. M., Brunger, A. T. and Clore, G M. (1988). Determination of three-dimensional structures of proteins by simulated annealing with interproton distance restraints Application to crambin, potato carboxypeptidase inhibitor and barley serine proteinase inhibitor 2. Protein Eng. 2, 27-38. 

Marryott, R. A., Dougherty, D. E., and Stollar, R. L. (1993). "Optimal groundwater management - 2. Application of simulated annealing to a field-scale contamination site." Water Resour. Res., 29(4), 847-860. 

Wang, M., and Zheng, C. (1998). "Application of genetic algorithms and simulated annealing in groundwater management formulation and comparison." J. AWRA, 34(3), 519-530. 

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