Gaussian Sphere Molecular Shape Comparison
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Solution Overview
Problem
Conventional methods for calculating molecular shape and comparing drug molecules are plagued by prolonged calculation times and decreased accuracy due to the discontinuity of the derivative of the volume obtained through the hard sphere model.
Innovation Solution
The method involves converting three-dimensional structure information into Gaussian spheres with radii equal to van der Waals radii, calculating overlap volumes and weights, and using these to determine self- and intermolecular volumes for accurate shape comparison, with constants k and k' ranging between 0.5 and 1.0 to optimize calculations.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If the hard sphere model is used to calculate molecular volume, then the calculation method is simple, but the derivative discontinuity causes prolonged calculation time and decreased accuracy
Solution Approach 1:
The patent transforms the hard sphere volume calculation into a Gaussian sphere volume calculation by changing the mathematical model parameter. The Gaussian function provides continuous derivatives while maintaining the ability to represent atomic volumes, thus improving calculation accuracy and efficiency without sacrificing the simplicity of the approach
Solution Approach 2:
The patent replaces the mechanical hard sphere model with a mathematical Gaussian function model. This substitution eliminates the discontinuity problem inherent in hard sphere boundaries while maintaining the physical interpretation of atomic volumes, enabling more efficient and accurate shape comparisons
2Measurement precision
If the hard sphere model with inclusion and exclusion terms is used for accurate volume calculation, then measurement precision improves, but device complexity and calculation complexity increase
Solution Approach 1:
By changing from hard sphere parameters to Gaussian parameters, the patent achieves accurate volume calculations through a single continuous function rather than complex inclusion-exclusion terms, reducing computational complexity while maintaining precision
Solution Approach 2:
The Gaussian function naturally handles overlap regions through its continuous decay, providing sufficient accuracy without requiring the excessive complexity of higher-order inclusion and exclusion terms that would be needed in the hard sphere model
Data Source
AI summary
The invention relates to a calculating method for molecular volume and shape comparison of two molecules. The method includes steps of loading in three-dimensional structure information of a first molecule, the three-dimensional structure information comprising type and coordinate values of each atom contained in the first molecule; obtaining respective van der Waals radius based on the type of respective atom contained in the first molecule, converting the three-dimensional structure information into a group of Gaussian spheres representing atoms in the first molecule; calculating overlap volume for each pair of Gaussian spheres; calculating the weight of each Gaussian sphere; calculating self-overlap volume of the first molecule, the self-overlap volume being used as a volume of the first molecule. The present invention is useful mathematical expression of molecular shape, shape comparison of drug molecules, and pharmacophore comparison of drug molecules, which comparisons, in turn, useful for virtual screening of drug molecules.