On this page is available a list of sources for further information (collected by class):

• [Amenta, Bern, Kamvysselis 1998] N. Amenta, M. Bern, and M. Kamvysselis "A new voronoi-based surface reconstruction algorithm." Proceedings of SIGGRAPH 98, pages 415--422, July 1998.
• [Barber 1996] Barber, C. B.; Dobkin, D. P.; Huhdanpaa, H. 1996. A Quickhull Algorithm for Convex Hulls. ACM Trans. Math. Soft. 22(4):469-483
• [Bondi 1964] Bondi, A. 1964. Van der Waals volumes and radii. J. Phys. Chem. 68:441-451
• [Bystroff 2001] Bystroff Christopher. 2001. "Masker:Improved Solvent Excluded Molecular Surafce Area Estimations using Boolean Masks", Renesseler Institute of Polytechnic, Troy, NY.
• [Connolly 1983a] Connolly, M. L. 1983. "Analytical Molecular Surface Calculation", Journal of Applied Crystallography 16, Pages 548-558.
• [Connolly 1983b] Connolly, M. L. 1983. "Solvent- accessible surfaces of proteins and nucleic acids", Science, Pages 709-713.
• [Connolly 1985a] Connolly, M. L. 1985. Molecular Surface Triangulation. J. Appl. Cryst. 18:499-505
• [Connolly 1985b] Connolly, M. L. 1985. Computation of Molecular Volume. J. Am. Chem. Soc. 107:1118-1124
• [Connolly 1993] Connolly, M. L. 1993. "The Molecular Surface Package", Journal of Molecular Graphics 11, Pages 139-141.
• [Connolly 1996] Connolly, M. L. 1996 Molecular Surfaces: A review
• [Eisenhaber 1993] Eisenhaber, F.; Argos P. 1993. Improved Strategy in Analytic Surface Calculation for Molecular Systems: Handling of Singularities and Computational Efficiency. 14:1272-1280
• [Eisenhaber 1995] Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander & Michael Scharf. The Double Cube Lattice Method: Efficient Approaches to Numerical Integration of Surface Area and Volume and to Dot Surface contouring of Molecular Assemblies. Journal of Computational Chemistry, volume 16, N3, pp.273-284 (1995)
• [Goede, Preissner, Frommel 1997] A. Goede, R. Preissner, C. Frommel: "Voronoi Cell: New Method for Allocation of Space among Atoms: Elimination of Avoidable Errors in Calculation of Atomic Volume and Density" Journal of Computational Chemistry, 18:1113-1123, 1997
• [Guibas, Stolfi 1985] Guibas, L. and Stolfi, J., "Primitives for the Manipulation of General Subdivisions and the Computation of Voronoi Diagrams" ACM transactions on Graphics, 4:74-23, April 1985.
• [Klein 1990] Klein, T. E. et al. 1990. A real-time malleable molecular surface. J. Mol. Graph. 8:16-24
• [Lee & Richards 1971] Lee, B. & Richards, F. M. (1971). .The Interpretation of Protein Structures: Estimation of Static Accessibility,. J. Mol. Biol. 55, 379-400.
• [LeGrand & Merz 1993] LeGrand S. M. & Merz, K. M. J. 1993. "Rapid Approximation to Molecular Surface Area via the Use of Boolean Logic and Look-up Tables", Journal of Computational Chemistry 14, Pages 349-52.
• [Pedretti, Villa, Vistoli 2002]. Pedretti, L. Villa, G. Vistoli: "Vega: A Versatile Program to Convert, Handle and Visualize Molecular Structure on windows-based PCs" J. Mol. Graph., Vol. 21, 47-49 (2002)
• [Perrot 1992] Perrot, G. et al. 1992. MSEED: A Program for the Rapid Analytical Determination of Accessible Surface Areas and Their Derivatives. J. Mol. Graph. 13:1-11
• [Sanner 1992] Sanner, M. F. 1992. "Modeling and Applications of Molecular Surfaces", Dissertation in University of Haute-Alsace, France.
• [Sanner 1995] Sanner, M. F., Olson, A. J., Spehner J.-C. 1995. "Fast and Robust Computation of Molecular Surfaces", 11th ACM Symposium on Computational Geometry.
• [Sanner 1996] Sanner, M. F., Olson A. J., Spehner J.-C. 1996. "Reduced Surface: An efficient Way to Compute Molecular Surfaces", Biopolymers 38(3), Pages 305-320.
• [Voorintholt 1989] Voorintholt, R.; Kosters, M. T.; Vegter, G. 1989. A very fast program for visualizing protein surfaces, channels and cavities. J. Mol. Graph. 7:243-245
• [Vorobjev 1997] Vorobjev, Y. N. 1997. SIMS: Computation of Smooth Invariant Molecular Surface. Biophys. J. 73:722-732

Rohit:

• M.C. Rivara and N. Hitschfeld: LEPP-Delaunay algorithm: a robust tool for producing size-optimal quality triangulations. Proceedings of the 8th Annual International Meshing Roundtable. October 1999, South Lake Tahoe, California, USA, pp: 205,220
  
• A. Goede, R. Preissner, C. Frommel: "Voronoi Cell: New Method for Allocation of Space among Atoms: Elimination of Avoidable Errors in Calculation of Atomic Volume and Density" Journal of Computational Chemistry, 18:1113-1123, 1997
  
• K. E. I. Hoff, T. Culver, J. Keyser, M. Lin, and D. Manocha: "Fast computation of generalized voronoi diagrams using graphics hardware." ACM SIGGRAPH, 1999.
  
• N. Amenta, M. Bern, and M. Kamvysselis: " A new voronoi-based surface reconstruction algorithm." Proceedings of SIGGRAPH 98, pages 415--422, July 1998.
  
• Guibas, L. and Stolfi, J., "Primitives for the Manipulation of General Subdivisions and the Computation of Voronoi Diagrams" ACM transactions on Graphics, 4:74-23, April 1985.
  
• A. Pedretti, L. Villa, G. Vistoli: "Vega: A Versatile Program to Convert, Handle and Visualize Molecular Structure on windows-based PCs" J. Mol. Graph., Vol. 21, 47-49 (2002)
  

Daniel:

Abagyan, Ruben A., and Totrov, Maxim M
The Contour-Buildup Algorithm to Calculate the Analytical Molecular Surface.
Journal of Structural Biology, Vol. 116, Article No. 0022, pg. 138-143 (1996)

Huitema, Henk, and van Liere, Robert
Time Critical Computing and rendering of Molecular Surfaces Using a Zonal Map.
Center for Mathematics and Computer Science CWI, Kruislaan 413, 1090 GB Amsterdam, the Netherlands

** Below are some references from the above journals**

Richards, F.M.
Areas, Volumes Packing and Protein Structure.
Ann. Rev. Biophysics. Bioengineering, 6:151-176, 1977.

Connolly, M.L.
Analytical Molecular Surface Calculation.
Journal of Applied Crystallography, 16:548-558, 1983

van Liere, R. and Mulder, J.D.
PVR - an architecture for portable vr applications.
In Gervautz M., Hildebrand A., and Schmalsteig D., editors, Virtual Environments '99, Proceedings of the Virtual Environments Conference & 5th Eurographics Workshop, pages 125-135. Springer Verlag, 1999.

** Below are some web references I found very helpfull **

Scientific and Artistic Uses of Molecular Surfaces

Measuring the Accuracy of Protein Models - Use of Contact Area Difference (CAD)

Visual Implementation of Fortune's Algorithm

A good reference for Representation of Molecular Surfaces and Rendering Techniques

Papers and Journal Articles:

• Bystroff Christopher, "Masker:Improved Solvent Excluded Molecular Surafce Area Estimations using Boolean Masks", Renesseler Institute of Polytechnic, Troy, NY, 2001.
• LeGrand, S. M. & Merz, K. M. J., "Rapid Approximation to Molecular Surface Area via the Use of Boolean Logic and Look-up Tables", Journal of Computational Chemistry 14, Pages 349-52, 1993.
• Connolly, M. L., "Analytical molecular surface calculation", Journal of Applied Crystallography 16, Pages 548-558, 1983a.
• Connolly, M. L., "Solvent-accessible surfaces of proteins and nucleic acids", Science, Pages 709-713, 1983b.
• Connolly, M. L., "The Molecular Surface Package", Journal of Molecular Graphics 11, Pages 139-141, 1993.
• Sanner, M. F., Olson A. J. and Spehner J.-C., "Reduced Surface: An efficient Way to Compute Molecular Surfaces", Biopolymers 38(3), 305-320, 1996.
• Sanner, M. F., Olson A. J. and Spehner J.-C., "Fast and robust computation of molecular surfaces", 11th ACM Symposium on Computational Geometry, 1995.
• Sanner, M. F., "Modeling and Applications of Molecular Surfaces", Dissertation in University of Haute-Alsace, France, 1992.
• Connolly, M. L., Molecular Surfaces: A review, 1996.

• Molecular Surface Calculation (Michel Sanner)

• Molecular Surfaces: A Review (Michael L. Connolly)

• Delaunay Triangulation

• Computational Geometry

• Divide and Conquer Algorithm (Tim Lambert)

• A Divide and Conquer Algorithm for Voronoi Diagrams of Polygons (Jordan Smith)

• Distributed molecular surface (DMS) package by Conrad Huang

• Available CGL software (includes DMS and PDB record I/O libraries)

• Scientific Software for FREE

Vince Stanev:

Frank Eisenhaber & Patrik Argos
"Improved Stategy in Analythic Surface Calculation for Molecular Systems: Handling of Singularities and Computational Efficiency"
Journal of Computational Chemistry, volume 14, N11, pp.1272-1280 (1993)

Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander & Michael Scharf
"The Double Cube Lattice Method: Efficient Approaches to Numerical Integration of Surface Area and Volume and to Dot Surface contouring of Molecular Assemblies"
Journal of Computational Chemistry, volume 16, N3, pp.273-284 (1995)

Peter Zhivkov:

• Vorobjev, Y. N. 1997. SIMS: Computation of Smooth Invariant Molecular Surface. Biophys. J. 73:722-732
• Connolly, M. L. 1985. Molecular Surface Triangulation. J. Appl. Cryst. 18:499-505
• Connolly, M. L. 1985. Computation of Molecular Volume. J. Am. Chem. Soc. 107:1118-1124
• Connolly, M. L. 1983. Analytical Molecular Surface Calculation. J. Appl. Crsyt. 16:548-558
• Eisenhaber, F.; Argos P. 1993. Improved Strategy in Analytic Surface Calculation for Molecular Systems: Handling of Singularities and Computational Efficiency. 14:1272-1280
• Klein, T. E. et al. 1990. A real-time malleable molecular surface. J. Mol. Graph. 8:16-24
• Voorintholt, R.; Kosters, M. T.; Vegter, G. 1989. A very fast program for visualizing protein surfaces, channels and cavities. J. Mol. Graph. 7:243-245
• Perrot, G. et al. 1992. MSEED: A Program for the Rapid Analytical Determination of Accessible Surface Areas and Their Derivatives. J. Mol. Graph. 13:1-11
• Sanner, M. F.; Olson, A. J.; Jean-Claude Spehner. 1995. Fast and Robust Computation of Molecular Surfaces. Proc. 11th ACM Symp. Comp. Geom, C6-C7.
• Barber, C. B.; Dobkin, D. P.; Huhdanpaa, H. 1996. A Quickhull Algorithm for Convex Hulls. ACM Trans. Math. Soft. 22(4):469-483
• Preparata, D. F., Shamos, M. 1988. Computational Geometry: An Introduction. Springer-Verlag, Berlin