R1nc R2 R3nh2 H

Based on the Ugi reaction, combinatorial libraries with four different R-groups can be created. After the reaction, all library molecules have the core shown on the right in common but differ in the four R-groups attached to it.

molecules have the core shown on the right in common but differ in the four R-groups attached to it.

the second phase is to improve the overall ranking of the solutions and to identify the correct placement. The placements are first energy-minimized using the CHARMm force field. For re-ranking, the software package CAMLab [117] is used. The final score consists of three contributions, a force field energy, an electrostatic part, and a nonpolar part of the solvation energy. The electrostatic part of the solvation energy is calculated by solving the Poisson equation using fast multigrid methods, while the nonpolar part is approximated by the total solvent-accessible surface.

Continue reading here: Docking of combinatorial libraries

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