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A general and robust ray-casting-based algorithm for triangulating surfaces at the nanoscale.

Sergio Decherchi1, Walter Rocchia

  • 1Department of Drug Discovery and Development, Istituto Italiano di Tecnologia, Genoa, Italy.

Plos One
|April 12, 2013
PubMed
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We developed a robust ray-casting method for triangulating complex molecular surfaces in nano-bioscience. This efficient approach, implemented in NanoShaper, accurately estimates surface area, volume, and detects cavities, outperforming existing methods.

Area of Science:

  • Computational nano-bioscience
  • Computational chemistry
  • Molecular modeling and simulation

Background:

  • Accurate triangulation of complex molecular surfaces is crucial for nano-bioscience applications.
  • Existing methods often struggle with robustness, efficiency, and handling diverse surface definitions.
  • There is a need for advanced computational tools to analyze nanometric systems.

Purpose of the Study:

  • To present a general, robust, and efficient ray-casting-based approach for triangulating complex manifold surfaces.
  • To integrate this method into a comprehensive framework for molecular surface analysis.
  • To provide a publicly available software suite (NanoShaper) for these capabilities.

Main Methods:

  • A novel ray-casting algorithm for surface triangulation, enhanced by the CGAL library.

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  • Implementation within the NanoShaper software, supporting multiple surface definitions (SES, Skin, Gaussian).
  • Integration with Poisson-Boltzmann solvers (DelPhi) and performance benchmarking against existing algorithms (MSMS, EDTSurf, Kruithof).

    • Main Results:

    • The NanoShaper suite demonstrates robustness against rotation, scale, and atom displacement, excelling in cavity detection.
    • Significantly improved triangulation speed compared to existing methods, especially for large molecular systems.
    • Superior performance in grid coloring compared to DelPhi's counterpart for Solvent Excluded Surface (SES).

    Conclusions:

    • The presented ray-casting approach provides a robust and efficient solution for triangulating complex manifold surfaces in nano-bioscience.
    • NanoShaper offers a versatile platform for molecular surface analysis, including area/volume estimation and cavity detection.
    • The method is scalable and effective even for very large biomolecular systems like the human adenovirus.