Refinement by simulated annealing

FIGURE 10.12. Diagram of a local and global minimum during refinement. Not that the ordinates are the R vale in the least-squares refinement, or the energy in the simulated annealing refinement. This emphasizes that the R value is not the only indicator of the correctness of a structure that can be used. 

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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... 

XPLOR is a modern package of refinement programs that includes powerful procedures for energy refinement by simulated annealing, in addition to more traditional tools like least-squares methods and molecular-replacement searches. The package is available for use on many different computer systems. Simulated annealing for large molecules usually requires supercomputers. 

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. 

Briinger, A. T., Krukowski, A., and Erickson, J. W. Slow-cooling protocols for crystallographic refinement by simulated annealing. Acta Cryst. A46, 585-593 (1990). 

Molecular dynamics can be coupled to a heat bath (see below) so that the resulting ensemble asymptotically approaches that generated by the Metropolis Monte Carlo acceptance criterion (Eq. 10). Thus, molecular dynamics and Monte Carlo are in principle equivalent for the purpose of simulated annealing although in practice one implementation may be more efficient than the other. Recent comparative work (Adams, Rice, Brunger, in preparation) has shown the molecular dynamics implementation of crystallographic refinement by simulated annealing to be more efficient than the Monte Carlo one. 

Divide and Conquer for Semiempiricai MO Methods Drug Design Linear Scaiing Methods for Eiectronic Structure Calculations Macromolecular Structure Calculation and Refinement by Simulated Annealing Methods and Applications Parallel Processing for Ab Initio Quantum Mechanical Methods. 

MACROMOLECULAR STRUCTURE CALCULATION AND REFINEMENT BY SIMULATED ANNEALING 1525... 

Macromolecular Structure Calculation and Refinement by Simulated Annealing Methods and Applications... 

Refinement by Simulated Annealing Methods and Applications Macromolecular Structures Determined using NMR Data NMR Chemical Shift Computation Ab Initio NMR Chemical Shift Computation Structural Applications NMR Data Correlation with Chemical Structure NMR of Transition Metal Compounds. 

The other exciting use of simulations is in helping to refine experimental structures. Unlike small molecule X-ray studies, macromolecular crystallography and NMR lead to structures which are underdetermined and, thus, simulations can be useful in conjunction with the experimental data to refine/determine such structures. Structural refinement and analysis is covered by articles by Billeter Macromolecular Structures Determined using NMR Data), Brunger Macromolecular Structure Calculation and Refinement by Simulated Annealing Methods and Applications), Case NMR Refinement), and Miller Molecular Superposition). 

Crystallographic Refinement by Simulated Annealing Application to Crambin. 

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