Assignments

Spring 2008

Problem Set 1 (Due Monday, April 7)

• PDF
• Solutions (PDF) (updated version)

Problem Set 2 (Due Monday, April 14)

• PDF (updated version)
• Reading for problem 4B: Briggs, et al. "The stoichiometry of Gag protein in HIV-1" Nature Structural & Molecular Biology 11, 672 - 675 (2004)
• Solutions (PDF)

Problem Set 3 (Due Monday, April 21)

• PDF
• Solutions (PDF)

Problem Set 4 (Due Monday, April 28)

• PDF (updated version)
• Solutions (PDF)

Midterm Exam (Due Monday, May 5)

• PDF
• Midterm Resources Page
• Glossary (PDF)
• Solutions (PDF)
• Statistics:
  • Average: 245.02 (out of 330)
  • Standard Deviation: 43.78
  • Histogram

Problem Set 5 (Due Monday, May 12)

• PDF
• APOBEC3G PDB file
• ZIP file (PS5 PDF + PDB file + SPDBV Tutorial PDF)

• SwissPDB-related items:

  • SwissPDB Viewer for Mac OS X
    
  • SwissPDB Viewer for Windows (95/98/Me/NT/2000/XP/Vista)
    
  • Bi 1 SwissPDB Viewer tutorial and sample file
• Protein Structure Study Guide (PDF)
• Molecular Dynamics references:
  • Heterogeneity Even at the Speed Limit of Folding: Large-scale Molecular Dynamics Study of a Fast-folding Variant of the Villin Headpiece. D. Ensign, P. M. Kasson, and V. S. Pande. Journal of Molecular Biology (2007)
  • How well can simulation predict protein folding kinetics and thermodynamics? C. D. Snow, E. J. Sorin, Y. Rhee, and V. S. Pande. Annual Review of Biophysics & Biomolecular Structure (2005)
• Solutions (PDF)
• Example student responses to MD question.

Problem Set 6 (Due Monday, May 19)

• PDF
• Solutions (PDF)

Problem Set 7 (Due Tuesday, May 27)

• PDF
• Paper for Problem #2: Cumming, et al. "Error Bars in Experimental Biology" JCB (2007).
• Glossary of immunological terms
• Solutions (PDF)

Problem Set 8 (Due Tuesday, June 3)

• PDF
• iPS reading for problem 1:
  5 things to know before jumping on the iPS bandwagon. David Cyranoski, Nature 452, 406-408 (2008)

Final Exam (Due Wednesday, June 11)

• Final Exam Resources Page
• Final Exam (ZIP of all necessary files)
• Individual final files:
  • PDF
  • Fasta file for problem 1: rt.fa
  • PDB files for problem 3:
    • groove.pdb
    • HLA.pdb
• Statistics:
  • Average:
    • Entire class: 286.13 (out of 400)
    • P/F grading scheme: 263.51
    • Letter grading scheme: 323.50
  • Standard Deviation:
    • Entire class: 52.19
    • P/F: 46.29
    • Letter grades: 38.12
  • Histogram (entire class)