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A very fast program for visualizing protein surfaces, channels and cavities.

R Voorintholt1, M T Kosters, G Vegter

  • 1Department of Computer Science, University of Groningen, The Netherlands.

Journal of Molecular Graphics
|December 1, 1989
PubMed
Summary
This summary is machine-generated.

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This study introduces a fast method for visualizing molecular surfaces using a grid-based distance calculation. It efficiently generates van der Waals and solvent-accessible surfaces without recalculations for different probe sizes.

Area of Science:

  • Computational chemistry
  • Molecular modeling
  • Structural biology

Background:

  • Visualizing molecular surfaces is crucial for understanding molecular interactions.
  • Existing methods for generating van der Waals and solvent-accessible surfaces can be computationally intensive.
  • Dynamic visualization of these surfaces aids in drug design and molecular analysis.

Purpose of the Study:

  • To develop a rapid and efficient method for visualizing molecular surfaces.
  • To enable on-the-fly generation of van der Waals and solvent-accessible surfaces.
  • To avoid computationally expensive recalculations for varying probe radii.

Main Methods:

  • A grid-based approach is employed to store the distance to the nearest atom.
  • Three-dimensional (3D) contouring is performed using molecular graphics software (e.g., FRODO).

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  • The method calculates distances on-the-fly for surface generation.

    • Main Results:

    • The described method achieves high-speed visualization of molecular surfaces.
    • It successfully generates accurate representations of van der Waals surfaces.
    • Solvent-accessible surfaces can be visualized without the need for recalculations when changing probe radius.

    Conclusions:

    • This grid-based method offers a significant speed improvement for molecular surface visualization.
    • It provides a flexible and efficient way to explore different molecular surface representations.
    • The technique is valuable for interactive molecular graphics and analysis.