Way of modeling intermolecular interactions and based on these methods for predicting Binding ligand molecules to a target molecule

摘要

FIELD: medicine, bio-technology, physics.;SUBSTANCE: methods for modeling process of connection of ligand molecule and target molecule are based on adjustment of several values for results of experimental alteration of values, characterizing connection process. Molecular-dynamic modeling method is based on adjustment of lesser number of parameters for experiment, but requires significant computer time resources, because it is necessary to detect movement trajectories of all atoms included in ligand molecule and target molecule during registration of their heat movement. Molecular-mechanical method includes greater number of parameters, determined by experiment, but requires only to perform optimization of full energy of system of interacting ligand molecule and target molecule. Both modeling methods consider effect of solvent, in which connection process can take place, while solvent is modeled either in apparent way by inserting solvent molecules into system, or in implicit way, when solvent is substituted with continuous environment with given characteristics like dielectric penetrability and conductivity. Both modeling methods are based on determining classic potentials of interaction between atoms of ligand molecule and target molecule using highly precise non-empiric quantum-mechanical calculations.;EFFECT: provision of required precision of created interaction potentials and simplified processing with use of analytical expressions for interaction potentials, providing possible fast numeric processing during molecular-dynamic modeling.;4 cl, 11 dwg, 3 tbl