COMPUTER-BASED MODELLING OF LIGAND/RECEPTOR STRUCTURES

摘要

Method for defining a binding site in biological macromolecule based on two-sphere grid and method for determining the free energy of ligand/RNA structure based on pseudo-energy values. These methods can be use in docking and also in high-throughput in silico screening of ligand libraries against RNA structures. Defining the binding site involves: (a) placing a grid over a 3D representation of the receptor; (b) identifying as an excluded volume grid point(s) which lie within the receptor; (c) centring a large sphere over grid point(s) and removing the grid points within the sphere if it does not overlap with the receptor; (e) centring a small sphere over all remaining grid points and determining whether one or more grid points within the small sphere overlap with the excluded volume of the receptor and identifying any non-overlapping grid points as representing a putative binding site cavity within the receptor.