Molecular Modeling and Simulation: An Interdisciplinary Guide

Tamar Schlick

• Assignment 1

  Sequence and Structural Databases, Molecular Modeling Perfective (Postscript, pdf);
  
  

• Assignment 2

  Introduction to the Insight II Modeling Package and the pdb File Structure and Retrieval (Postscript, pdf);
  
  

• Assignment 3

  Construction and Analysis of the Pentapeptide Met-enkephalin with the Insight II Program (Postscript, pdf);
  
  

• Assignment 4

  Creating Ramachandran Plots from Known Protein Structures and the NDB (Postscript,pdf)
  
  • Fortran program for selecting Ala, Ile, Val, and Leu data   aa_select.f
  • Database of 50 proteins: Download tar file
  
  

• Assignment 5

  Analysis of Protein/DNA Complexes with Insight and NDB:
  Canonical vs. Protein/Bound DNA, and DNA/Protein Interactions (Postscript, pdf);
  
  

• Assignment 6

  MIDTERM: Homology Contest! (Postscript, pdf);
  Exploring Sequence/Structure/Function Relationships (Related Tools/Databases like SCOP, IMAGE, BLAST, NDB, PDB)
  
  

• Assignment 7

  Molecular Mechanics Force Fields:
  Approximations, Variations, and the Assessment of Results with respect to Experiment and other Simulations (Postscript, pdf);
  
  

• Assignment 8

  A Bit of Programming: Nonbonded Versus Bonded Energy Computations} (Postscript, pdf);
  
  • Segments from molecular mechanics subprograms for molecules  mm.f
  • XYZ coordinates of a polymer of 1000 atoms Download file
  
  

• Assignment 9

  TERM PROJECT: The Successes (Failures?) of Molecular Modeling (Postscript, pdf)
  
  

• Assignment 10

  Experiments in Molecular Geometry Optimization: Biphenyl Minimization (Postscript, pdf)
  
  • Coordinates of a biphenyl molecule: biphenyl.car
  • Coordinates of a distorted biphenyl molecule: biphenyl_distorte.car
  
  

• Assignment 11

  A Global Optimization Contest! (Postscript, pdf)
  
  

• Assignment 12

  Monte Carlo Simulations (Postscript, pdf)
  Programs to test the RANDU random generator in two and three dimentions:
  
  • Test the RANDU random number generator in 2D  randu2D.f
  • Test the RANDU random number generator in 3D  randu3D.f
    
  
  

• Assignment 13

  Advanced Exercises in Monte Carlo and Minimization Techniques (Postscript, pdf)
  
  

• Assignment 14

  Advanced Exercises in Molecular Dynamics (Postscript, pdf)
  
  

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