Molecular Surfaces and Volumes

Molecular Surface Programs

• ACCESS: Program written by B. Lee, F.M. Richards and M. Handschumacher. For each atom in a list the program ACCESS is designed to find the surface area in square Angstroms that is accessible to a probe sphere of a radius specified by the user.
  • Surface accessibility.
• Argos-ASC: The Analytic Surface Calculation Package for Molecular Systems. Collection of tools for Surface and Volume Calculation.
  • Argos-ASC.
• CONSCRIPT: A program for generating electron density isosurfaces for presentation in protein crystallography.
  • Home Page.
  • Sample Image.
• GETAREA: Calculation of solvent accesible surface areas, atomic solvation energies and their gradients for macromolecules.
  • Manual.
• HARMONY: B.S. Duncan (Molecular Graphics Laboratory): Spherical Harmonic Representations of Molecular surfaces.
  • Home Page.
• Molviewer-ogl: Molecular graphics software developed at York by M. Hartshorn. Molecular Surfaces can be generated for all or part of a molecular structure.
  • Molviewer-ogl.
  • Construction of a partial molecular Surface: GIF Image 600x400pixels.
• MSMS: Molecular Surfaces Calculation by M. Sanner. MSMS allows to compute triangulations of Solvent Excluded Surfaces.
  • MSMS Home Page
• MSP: Molecular Surface Package. Copyright 1996 by M.L. Connolly.
  • MSP: User Manual.
• MSV: Molecular Surface Viewer. MSV is an OpenGL based viewer for molecular surfaces computed with MSMS.
  • Home Page.
• NACCESS: Atomic Solvent Accessible Area Calculations.
  • Home Page.
• SURFNET: Program generates generates surfaces and void regions between surfaces from coordinate data supplied in the PDB file.
  • Home Page.

Molecular Volumes

• PROVE: Protein Volume Evaluation.
• VOLUME: Residue Voronoi Volumes.

References Online

• ``Molecular Surfaces: A Review'', by M.L. Connolly.
• The Science and Art of Molecular Surfaces: The Scientific and Artistic Uses of Molecular Surfaces, by T.J. O'Donnel.
• ``Shape Analysis of Protein Surfaces'', by B. Duncan and A. Olson (1991), Research Institute of Scripps Clinic.

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