The protein search algorithm by the computer in order to identify the binding site

摘要

Provided is a computer implemented method of analyzing a macromolecule for potential binding sites, comprising: positioning an instance of a computer representation of an organic fragment at a plurality of potential binding sites of the macromolecule; selecting a value of B, wherein B = ~~/kT + ln&l t;N, where ~~ is the excess chemical potential, k is Boltzmann's constant, T is t he absolute temperature, and N is the mean number of molecules of the o rganic fragment; repositioning the instances of the organic fragment until a minimized energy state is obtained; assessing, for each instance of the repositioned organic fragment, whether the repositioned organic fragment bin ds to the macromolecule at the associated potential binding site at the selecte d value of B; deleting instances of the organic fragment that do not bind at t he associated potential binding site at the selected value of B; repeating thes e steps at a lesser value of B; and outputting a list of undeleted instances o f the organic fragment; provided that the organic fragment is not water./SDOA B