Conformational Space Annealing

AMI Semiempirical Austin method 1 CSA Conformational space annealing DFT Density functional theory DFTB Density-functional-based tight binding EA Evolutionary algorithm... 

Lee, J., Scheraga, H. A. and Rackovsky, S. (1997). New optimization method for conformational energy calculations on polypeptides Conformational space annealing. J. Comp. Chem., 18, 1222-1232. 

Lee, J., Liwo, A., and Scheraga, H. A., Energy-based de novo protein folding by conformational space annealing and an off-lattice united-residue force field application to the 10-55 fragment of staphylococcal protein A and to apo calbindin D9K, Proc. Natl Acad. ScL U.S.A., 96, 2025, 1999. 

The procedure also used random array initial structures for molecular dynamics algorithm using XPLOR-NIH.12 Sixteen thousand initial structures were subjected to an initial simulated annealing (5,000 K, 80 ps). This means that the initial structures did not cover the entire conformational space, but were randomly distributed all over the space. The conformational... 

J. Y. Lee and H. A. Scheraga, Conformational space annealing by parallel computations Extensive conformational search of met-enkephaUn and of the 20-residue membrane-bound portion of meUttin. Int. J. Quant. Chem. 75(3), 255—265 (1999). 

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. 

Model optimization is a further refinement of the secondary and tertiary structure. At a minimum, a molecular mechanics energy minimization is done. Often, molecular dynamics or simulated annealing are used. These are frequently chosen to search the region of conformational space relatively close to the starting structure. For marginal cases, this step is very important and larger simulations should be run. 

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). 

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