CS 89/189 | Computational Structural Biology

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Date	Topics	References	Due
Mar 27	Introduction to Protein Structure	The Protein Data Bank (PDB) Cormen et al., Intro to Algorithms, Ch. 15
Mar 29	Protein Structure Determination	The Protein Data Bank (PDB)
Apr 3	Protein Structure Prediction, Classics	Chou, Fasman, Biochemistry, 2(13):222 Bowie, Luthy, Eisenberg Science, 253(5016):164	Critiques
Apr 5	Protein Folding; Lecture on Protein Design	Lindorff-Larsen et al., Science, 344(6055):517 (2011), to be presented by Jonathan Connell Piana,et al. Biophysical Journal, 110(9):L47 (2011)	Critiques
Apr 10	Protein Folding & Design	Piana, et al. Biophysical Journal, 110(9):L47 (2011), to be presented by Fanghao Chen Kuhlman and Baker, PNAS, 97(19):10383 (2000), to be presented by Milka Doktorova	Critiques
Apr 12	Protein Design	Kuhlman et al. Science, 302(5649):1364 (2003), to be presented by David Kopec Reina et al., Nature Structural Biology, 9:621 (2002), to be presented by Rima Narayana Murthy	Critiques
Apr 17	CLASS CANCELED
Apr 19	CLASS CANCELED
Apr 24	Ab Initio Structure Prediction	Bradley et al. Science, 309(5742):1868 (2005), to be presented by Minjun Huang Cooper et al., Nature, 466:756 (2010), to be presented by Kevin Walker	Critiques
Apr 26	Ab Initio Structure Prediction	Khatib et al. PNAS, 108(47):18949 (2011), to be presented by Tucker Ward Ferron et al. Proteins, 65(1):1 (2006), to be presented by Fan Zheng	Critiques
May 1	Structure Prediction by Homology Modeling	Wallner et al. Protein Science, 14(5):1315 (2009), to be presented by Emery Coxe Zhang et al. PNAS, 102(4):1029 (2004), to be presented by Luke Fowlie	Critiques
May 3	Modeling Assemblies	Alber et al. Nature, 450:683 (2007), to be presented by Milo Johnson and Qinxin Pan	Critiques, Project Proposals
May 8	Transmembrane Protein Structure Prediction	Soto et al. JMB, 414(4):596 (2011), to be presented by Xiaoming He Barth et al. PNAS, 106(5):1409 (2009), to be presented by Jonathan Connell	Critiques
May 10	Structural Alignment and Similarity-based Search/Retreival	Zhang et al. Nucleic Acids Research, 33(7):2302 (2005), to be presented by Emery Coxe Budowski-Tal et al. PNAS, 107(8):3481 (2010), to be presented by Milka Doktorova	Critiques
May 15	Function Prediction, Protein Design	Jiang et al. Science, 319(5868):1387 (2008), to be presented by David Kopec	Critiques
May 17	Function Prediction, Structural Similarity Searching	He et al. RECOMB, (2012), to be presented by Fanghao Chen London et al. PLoS Computational Biology, 7(10): e1002170 (2011), to be presented by Minjun Huang	Critiques
May 22	Protein Design, Protein Structural Universe	Lanci et al. PNAS, 109(19):7304 (), to be presented by Kevin Walker Osadchy and Kolodny PNAS, 108(30):12301 (2011), to be presented by Rima Narayana Murthy	Critiques
May 24	Function Prediction	Blom et al. JMB, 249(5):1351 (1999), to be presented by Tucker Ward	Critiques
May 29	Final Project Presentations	Milo, Tucker; Fanghao, Xiaoming, Minjun; Luke, Emory; Qinxin; David	Critiques
May 30	Final Project Presentations	Fan; Jonathan; Milka, Rima, Kevin	Critiques

Upcoming topics: protein folding, protein design, structure preduction, function prediction, docking and binding, statistical mechanics.