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Interactive Molecular Model Assembly with 3D Printing
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Meshing molecular surfaces based on analytical implicit representation.

Chaoyu Quan1, Benjamin Stamm2

  • 1Sorbonne Universités, UPMC Univ Paris 06, UMR 7598, Laboratoire Jacques-Louis Lions, F-75005 Paris, France; CNRS, UMR 7598, Laboratoire Jacques-Louis Lions, F-75005 Paris, France.

Journal of Molecular Graphics & Modelling
|December 13, 2016
PubMed
Summary
This summary is machine-generated.

We present a novel algorithm for meshing molecular surfaces, including solvent accessible surface (SAS) and solvent excluded surface (SES). This method accurately characterizes SES singularities and fills molecular inner holes for comprehensive surface analysis.

Keywords:
Advancing-front methodImplicit representationMeshing algorithmMolecular surfaceMolecular visualizationSolvent excluded surface

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Area of Science:

  • Computational chemistry
  • Molecular modeling
  • Surface science

Background:

  • Accurate molecular surface representation is crucial for understanding molecular interactions.
  • Existing meshing algorithms face challenges with complex molecular surface features like singularities and inner holes.

Purpose of the Study:

  • To develop an efficient and accurate algorithm for meshing molecular surfaces.
  • To specifically address the challenges of solvent accessible surface (SAS) and solvent excluded surface (SES) meshing.
  • To enable a complete characterization of SES singularities and fill molecular inner holes.

Main Methods:

  • Patch-wise meshing approach.
  • Advancing-front method adapted for molecular surfaces.
  • Utilizing a novel analysis of SES to a priori describe singularities.
  • Algorithm for filling molecular inner holes based on pre-computed surface data structures.

Main Results:

  • A robust algorithm for generating surface meshes for SAS and SES.
  • Complete characterization of SES singularities.
  • Successful implementation of an algorithm to fill molecular inner holes.
  • Improved accuracy and completeness in molecular surface representation.

Conclusions:

  • The developed algorithm provides a significant advancement in molecular surface meshing.
  • The approach enables more detailed and accurate analysis of molecular surfaces.
  • This method has potential applications in various fields requiring precise molecular geometry.