Multiple-copy simultaneous search methods

Miranker A, Karplus M. Functionality maps of binding sites a multiple copy simultaneous search method. Proteins 1991 11 29-34. 

Maps of Binding Sites A Multiple Copy Simultaneous Search Method. 

Miranker A and M Karplus 1991. Functionality Maps of Binding Sites - A Multiple Copy Simultaneous Search Method. Proteins Structure, Function and Genetics 11 29-34. 

To overcome the limitations of the database search methods, conformational search methods were developed [95,96,109]. There are many such methods, exploiting different protein representations, objective function tenns, and optimization or enumeration algorithms. The search algorithms include the minimum perturbation method [97], molecular dynamics simulations [92,110,111], genetic algorithms [112], Monte Carlo and simulated annealing [113,114], multiple copy simultaneous search [115-117], self-consistent field optimization [118], and an enumeration based on the graph theory [119]. 

A somewhat different approach has been implemented in MCSS (multiple copies simultaneous search) [10]. In this method, up to 5000 copies of a functional group are randomly distributed in the binding pocket and simultaneously minimized by a force field. The simultaneous optimization is performed in... 

Joseph-McCarthy, D., Hogle, J. M. and Karplus, M. (1997). Use of the multiple copy simultaneous search (MCSS) method to design a new class of picomavirus capsid binding drugs. Proteins, 29, 32-58. 

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