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SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions

R A Laskowski1

  • 1Department of Biochemistry and Molecular Biology, University College, London, England. roman@bsm.bioc.ucl.ac.uk

Journal of Molecular Graphics
|October 1, 1995
PubMed
Summary
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The SURFNET program identifies molecular surfaces and voids, aiding in protein active site visualization. This computational tool enhances understanding of molecular interactions and internal cavities.

Area of Science:

  • Computational chemistry
  • Structural biology
  • Molecular modeling

Background:

  • Understanding molecular structure and interactions is crucial in drug discovery and biological research.
  • Identifying active sites and voids within proteins is key to understanding their function.

Purpose of the Study:

  • To introduce the SURFNET program for generating molecular surfaces and gap regions.
  • To demonstrate its utility in visualizing protein active sites and molecular voids.

Main Methods:

  • Utilizes 3D coordinates from PDB files to generate molecular surfaces.
  • Identifies and delineates gap regions, including inter-molecular voids and intra-molecular cavities.
  • Generates 3D contour surfaces for arbitrary 3D data point distributions.

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Main Results:

  • SURFNET effectively generates molecular surfaces and identifies significant void spaces.
  • The program clearly delineates protein active site regions.
  • Output surfaces are compatible with major molecular modeling and graphics packages for interactive visualization.

Conclusions:

  • SURFNET is a valuable tool for visualizing molecular surfaces, voids, and protein active sites.
  • Its interactive visualization capabilities enhance the study of molecular structures and interactions.
  • The program supports various output formats for broad applicability in computational and structural biology.