Algorithms for Molecular Docking

A Comparison of Heuristic Search Algorithms for Molecular Docking. 

In the previous sections, the algorithms for molecular docking and their performance on example data were discussed. In practical applications... 

D. R. Westhead, D. E. Clark, and C. W. Murray. A comparison of heuristic search algorithms for molecular docking. Journal of Computer-Aided Molecular Design, 11 209-228, 1997. 

Jones G, P Willett, R C Glen, A R Leach and R Taylor 1997. Development and Validation of a Geneti Algorithm for Flexible Docking. Journal of Molecular Biology 267 727-748. 

Owing to the much longer per-molecule computing time, exploiting the structure of combinatorial libraries becomes much more important for molecular docking algorithms. 

Taylor. Development and validation of a genetic algorithm for flexible docking. Journal of Molecular Biology, 267 727—748, 1997. 

Jones, G., Wdlett, P., Glen, R.C., Leach, A.R., and Taylor, R. (1997) Development and validation of a genetic algorithm for flexible docking. Journal of Molecular Biology, 267, 727-748. 

S. R. Kilvington and A. R. Leach, Molecular Graphics Society Meeting, University of York, UK, March 28, 1993. An Algorithm for Connecting Docked Fragments. 

Genetic algorithms can also be used to perform molecular docking [Judson et d. 1994 Jont et d. 1995b Oshiro et d. 1995]. Each chromosome codes not only for the internal conform tion of the ligand as described in Section 9.9.1 but also for the orientation of the ligand withi the receptor site. Both the orientation and the internal conformation will thus vary as th populations evolve. The score of each docked structure within the site acts as the fitnes function used to select the individuals for the next iteration. 

TJA Ewing, ID Kuntz. Critical evaluation of search algorithms for automated molecular docking and database screening. J Comput Chem 18 1175-1189, 1997. 

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