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• Course Syllabus
• Introduction
• Assignments
• Course Webpage
  
  

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• FINAL PRESENTATION ON DEC 13

• CLASS PRESENTATION ON NOV 8

• Project Critique and Scientific Explanation (added Nov 15)

• About MASKER (added Nov 22)

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  Delaunay Triangulation using Divide and Conquer algorithm

• 4INS.txt
• CAs.txt
  
  
• Delaunay Triangulation Package
  
  
• CarbonAlpha Delaunay Triangulation using Divide and Conquer Package
• Delaunay Triangulation for 1000 points
• Delaunay Triangulation for 2000 points
• Delaunay Triangulation for 3000 points
• Delaunay Triangulation for 4000 points
• Delaunay Triangulation for 5000 points
• Delaunay Triangulation for 6000 points
• Delaunay Triangulation for 7000 points

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  Molecular Surface Calculation using DMS

• Distributed molecular surface (DMS) package by Conrad Huang
• Available CGL software (includes DMS and PDB record I/O libraries)
• DMS package

  Tests Files: 140D.pdb 16VP.pdb 1A4G.pdb 4INS.pdb 1a34.pdb 1h1k.pdb 1HVU.pdb 1I84.pdb 1IAS.pdb 1jmu.pdb 2btv.pdb 4HMG.pdb 1AFV.pdb 148d.pdb None4.pdb unknown.pdb	Test Output: result_140D result_16VP result_1A4G result_4INS result_1a34 result_1h1k result_1HVU result_1I84 result_1IAS result_1jmu result_2btv result_4HMG result_1AFV result_148d result_None4 result_unknown

  
  Table of results
  Graph_Overview
  Graph

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  Molecular Surface Calculation using MASKER

• MASKER by Chris Bystroff
• MASKER package

  Tests Files: 140D.pdb 16VP.pdb 1A4G.pdb 4INS.pdb 1a34.pdb 1h1k.pdb 1HVU.pdb 1I84.pdb 1IAS.pdb 1jmu.pdb 2btv.pdb 4HMG.pdb 1AFV.pdb 148d.pdb None4.pdb unknown.pdb	Test Output: result_140D result_16VP result_1A4G result_4INS result_1a34 result_1h1k result_1HVU result_1I84 result_1IAS result_1jmu result_2btv result_4HMG result_1AFV result_148d result_None4 result_unknown

  
  Table of results
  Graph_Overview
  Graph

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  Important links:

  • 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)
  • Collection of Papers by Chris Bystroff
  • Collection of Papers by Ruben Abagyan Research Group
  • Download a free demo version of Prism and try it with your own data
  • DataFit Curve Fitting and Data Plotting Software by Oakdale Engineering

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  Some Papers that I found:

  • Improved solvent excluded molecular surface area estimation using Boolean masks by Chris Bystroff
  • The Contour-Buildup Algorithm to calculate the Analytical Molecular Surface

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  Here are some carbon notes

  Believe me, you can get Scientific Software for FREE

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  Bibliography

• 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