Patent Document ID: 20110066384
Application ID: 12904968
Patent Status: 0

Claim One:
1. A method for determining molecular shape of a receptor comprising: having a first molecule with a determined solvent-accessible molecular surface solvent-accessible molecular surface, wherein said surface is a receptor which can be visualized by a processor; restricting said surface to said receptor's active site; visualizing said molecular surface as a plurality of small area elements; said processor performing a ray-trace, said ray-trace comprising: starting a ray at a start point in a first of said small area elements; propagating said ray in a first direction until said ray impacts a second of said small area elements at an impact point, resulting in an initial ray segment between said start point and said impact point; reflecting said ray from said impact point as if said molecular surface was perfectly reflective of said ray; recording characteristics of said ray segment, including electrostatic properties of said impact point and said start point; and repeating said steps of starting, propagating, reflecting, and recording for a new ray segment using said impact point as said start point of said new ray segment; and stopping said repeating prior to recording if a predetermined stop condition is met; storing said start points and said impact points and attributes of atoms associated thereto; corresponding said initial ray segment and said new ray segment to said atoms; partitioning said molecule into atom clusters; decomposing said ray trace by assigning said initial ray segment and said new ray segment according to results of said step of corresponding, wherein each said ray segment is assigned at least in fractional part to at least one segment corresponding to an atom cluster (an intra-cluster segment) or atoms between atom clusters (an inter-cluster segment); computing a unique probability distribution for each said intra-cluster segment and each said inter-cluster segment based on characteristics of said assigned ray segments, said probability distribution providing an indication of the shape of said inter-cluster segment or said inter-cluster segment; storing said probability distribution for later comparison to other probability distributions indicative of shapes of other molecules or portions thereof.