Riemannian Geometry and Molecular Surfaces I: Spectrum of the Laplacian

TL;DR

This paper introduces RGMolSA, a novel Riemannian geometry-based molecular shape descriptor that uses the spectrum of the Laplacian to compare molecular surfaces without alignment, showing promise in virtual screening.

Contribution

The paper develops RGMolSA, a new alignment-free, mesh-free shape descriptor derived from Riemannian geometry and spectral analysis, improving molecular shape comparison methods.

Findings

RGMolSA effectively captures surface shape using eigenvalues and surface area.

It performs well in distinguishing PDE5 inhibitors with similar shapes.

The method handles different molecular conformers reliably.

Abstract

Ligand-based virtual screening aims to reduce the cost and duration of drug discovery campaigns. Shape similarity can be used to screen large databases, with the goal of predicting potential new hits by comparing to molecules with known favourable properties. This paper presents the theory underpinning RGMolSA, a new alignment-free and mesh-free surface-based molecular shape descriptor derived from the mathematical theory of Riemannian geometry. The treatment of a molecule as a series of intersecting spheres allows the description of its surface geometry using the Riemannian metric, obtained by considering the spectrum of the Laplacian. This gives a simple vector descriptor constructed of the weighted surface area and eight non-zero eigenvalues, which capture the surface shape. We demonstrate the potential of our method by considering a series of PDE5 inhibitors that are known to have similar shape as an initial test case. RGMolSA displays promise when compared to existing shape descriptors and in its capability to handle different molecular conformers. The code and data used to produce the results are available via GitHub: https://github.com/RPirie96/RGMolSA.