Discussion sections

 

Discussion sections will be held every Thursday from 4-5PM and 6-7PM in BASS 205. Students are required to attend one of the two sessions.

 

Jan 21
 T.F. Smith and M.S. Waterman. (1981) Identification of common molecular subsequences. Journal of Molecular Biology,147(1): 195-7. PMID: 7265238. Article
Jan 28

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. (1990) Basic local alignment search tool. Journal of Molecular Biology, 215(3):403-10. PMID: 2231712. Article

Garnier J, Gibrat JF, Robson B. (1996) GOR method for predicting protein secondary structure from amino acid sequence.Methods in Enzymology,266: 540-53. PMID: 8743705. Article
Feb 11

ML Connolly. (1983) Solvent-accessible surfaces of proteins and nucleic acids. Science, 221(4612): 709-13. PMID: 6879170. Article

Martin Karplus and J. Andrew McCammon. (2002) Molecular dynamics simulations of biomolecules. Nature Structural Biology,9, 646-52. PMID: 12198485. Article
Feb 18

Cabrita LD, Dobson CM, Christodoulou J. (2010) Protein folding on the ribosome.Current Opinion in Structural Biology, In Press. Article

Dill KA, Ozkan SB, Shell MS, Weikl TR. (2008) The Protein Folding Problem.Annu Rev Biophys,9, 37:289-316. PMID: 2443096. Article
Feb 25

D. Bratko, T. Cellmer, J. M. Prausnitz, and H. W. Blanch, “Molecular Simulation of protein aggregation,” Biotechnology and Bioengineering 96 (2007) 1 [PDF]

W. C. Swope, J. W. Pitera, et al., "Describing protein folding kinetics by Molecular Dynamics Simulations. 2. Example applications to Alanine Dipeptide and beta-hairpin peptide," J. Phys. Chem. B 108 (2004) 6582 [PDF]

Mar 4

Jayachandran G, Vishal V, Pande VS. "Using massively parallel simulation and Markovian models to study protein folding: Examining the dynamics of the Villin headpiece,” J. Chem. Phys. 124 (2006) 164902 [PDF]

Bowman GR, Beauchamp KA, Boxer G, Pande VS. “Progress and challenges in the automated construction of Markov state models for full protein systems,” J. Chem. Phys. 131 (2009) 124101 [PDF]

Mar 25
 Perelson AS. Modelling viral and immune system dynamics. Nat Rev Immunol. 2002 Jan;2(1):28-36. [PDF]

Apr 1

Metzker ML. "Sequencing technologies - the next generation” Nature Reviews Genetics. 11 (2010) [PDF]

Neumann AU, Lam NP, Dahari H, Gretch DR, Wiley TE, Layden TJ, Perelson AS. “Hepatitis C viral dynamics in vivo and the antiviral efficacy of interferon-alpha therapy”, Science. (1998) Oct 2;282(5386):103-7. [PDF]

Apr 8

Wheeler DA et al. "The complete genome of an individual by massively parallel DNA sequencing,” Nature. 452:872-876 (208) [PDF]

Pepke S, Wold B, Mortazavi A. “Computation for ChIP-Seq and RNA-Seq studies”, Nature Methods. (2009) Nov.;6(11 Suppl)S22:33. [PDF]

 

 

Papers for Dr. O'Hern's Lectures:

  • J. D. Honeycutt and D. Thirumalai, “The nature of folded states
    of globular proteins,” Biopolymers 32 (1992) 695 [PDF]
  • W. C. Swope and J. W. Pitera, “Describing protein folding kinetics
    By molecular dynamics simulations. 1. Theory,” J. Phys. Chem. B 108
    (2004) 6571 [PDF]
  • W. C. Swope, J. W. Pitera, et al., "Describing protein folding kinetics by Molecular Dynamics Simulations. 2. Example applications to Alanine Dipeptide and beta-hairpin peptide," J. Phys. Chem. B 108 (2004) 6582 [PDF]
  • D. Bratko, T. Cellmer, J. M. Prausnitz, and H. W. Blanch, “Molecular Simulation of protein aggregation,” Biotechnology and Bioengineering 96 (2007) 1 [PDF]

 

Problem Sets (MB&B and MCDB):

 

Programming Assignments (CPSC and CBB):

 

Quiz Keys:

Slide Presentations from Discussion (Optional to Submit):

 

 

Related pages

Outline of Topics