Generation of Molecular Surfaces

Links and Papers:

• http://www.math.tau.ac.il/~rshamir/algmb/00/scribe00/html/lec13/node22

• Web Page:
  • http://www.biohedron.com/
• Papers About MSP:
  • M.L. Connolly (1983) "Analytical molecular surface calculation", J. Appl. Crystallogr. 16, 548-558.
  • M.L. Connolly (1983) "Solvent-accessible surfaces of proteins and nucleic acids", Science 221, 709-713.
  • M.L. Connolly (1985) "Molecular surface triangulation", J. Appl. Crystallogr. 18, 499-505.
  • M.L. Connolly (1986) "Measurement of protein surface shape by solid angles", J. Mol. Graphics 4, 3-6.
  • M.L. Connolly (1986) "Plotting protein surfaces", J. Mol. Graphics 4, 93-96.
  • M.L. Connolly (1993) "The molecular surface package", J. Mol. Graphics 11, 139-141

• Web Page
  • http://www.scripps.edu/pub/olson-web/people/sanner/html/msms_home.html
• Paper About MSMS:
  • M.F. Sanner, J.C. Spehner and A.J. Olson (1996) "Reduced surface: an efficient way to compute molecular surfaces", Biopolymers, Vol. 38, (3), 305-320.

• Web Page:
  • http://www.biochem.ucl.ac.uk/~roman/surfnet/surfnet.html
• Paper about SURFNET:
  • R.A. Laskowski (1995) "SURFNET: A program for visualizing molecular surfaces, cavities and intermolecular interactions", J. Mol. Graph., 13, 323-330.

• Web Page
  • http://ccvweb.csres.utexas.edu/ccv/projects/angstrom/sd/shape.php
• Paper:
  • C.L. Bajaj, V. Pascucci, A. Shamir, R.J. Holt, A.N. Netravali (1999) "Multiresolution Molecular Shapes" (1999)

• Web Page:
  • http://mendel.imp.univie.ac.at/SURFACE/ASC/asc2.html
• Papers about ASC:
  • F. Eisenhaber and P. Argos (1993) "Improved Strategy in Analytic Surface Calculation for Molecular Systems: Handling of Singularities and Computational Efficiency." Journal of Computational Chemistry, 14 (1993) N11, pp.1272-1280
  • F. Eisenhaber, P. Lijnzaad, P. Argos, C. Sander and M. Scharf (1995) "The Double Cubic Lattice Method: Efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies." J. Comp. Chem. 16(3): 273-284.

• S.L. Lin, R. Nussinov, D. Fischer, and H.J. Wolfson, (1994) "Molecular Surface Representation by Sparse Critical Points", PROTEINS, vol. 18, pp. 94-101, (1994)
• A. Varshney, F.P. Brooks, Jr., D.C. Richardson, W.V. Wright, D.Manocha, (1995) "Defining, Computing, and Visualizing Molecular Interfaces", IEEE Visualization '95
• Y.N. Vorobjev and J. HermansS (1997) "SIMS: Computation of a smooth invariant molecular surface", Biophysical Journal,73:722-732.
• D. Halperin, M.H. Overmars, (1994) "Spheres, Molecules, and Hidden Surface Removal", Symposium on Computational Geometry (1994)
• P.S. Heckbert and M. Garland, (1997), "A Survey of Polygonal Surface Simplification Algorithms", Multiresolution Surface Modeling Course, SIGGRAPH '97