Patch-Based Ray Tracing in NanoShaper Boosts Molecular Surface Computation.

ABSTRACT: NanoShaper (NS) is a widely used tool that leverages ray tracing for molecular surface triangulation, pocket detection, and supports Poisson-Boltzmann equation solvers. By retaining the established methodological framework and implementing a targeted redesign, our approach achieves performance gains of up to 12.5× and memory reductions of up to 8×, enabling the triangulation of complexes containing millions of atoms on relatively modest computational architectures in a short time. The key innovation is a patch-based ray tracing algorithm that replaces the traditional ray-sweeping approach. By iterating over surface patches rather than rays, this method enhances cache performance and removes the need for memory-intensive grids for patch localization, yielding major reductions in memory usag

SUBMITTER: Mazzeo MD 

PROVIDER: S-EPMC12801300 | biostudies-literature | 2026 Jan

REPOSITORIES: biostudies-literature