CS 86/186 | Computational Structural Biology

This page will be updated regularly with current/upcoming topics. Notes will be provided for each class, linked from the date. Notes and some materials are password-restricted with your Dartmouth login (DND). Feedback is appreciated—typos and broken links, suggestions for more detailed explanations, pointers to supporting materials on the web, etc.

Date	Topics	References	Out	Due
Jan 8	Intro to Proteins and Structure	Hunter, Intro to molecular biology for the computer scientist Protein Data Bank, PDB PyMOL installation, for Mac, and for Windows	SA1
Jan 10	Structural similarity and alignment	PDB structure alignment CATH structure classification Alignment programs: CE and FATCAT Literature: Shindyalov & Bourne (CE) and Ye & Godzik (FATCAT) PyMOL Wiki Python docs (including tutorial)	SA2	SA1
Jan 15	CLASS CANCELED
Jan 17	Energetics of Protein Structure, MD	CS cluster FAQ VMD NAMD NAMD tutorials	Lab 1	SA2
Jan 22	Intro to Stat Mech, ensembles
Jan 24	Improved integration methods, FEP			Lab 1
Jan 29	Structure prediction: Rosetta	Literature: Simons et al.; Rohl et al. Rosetta: Robetta server; PyRosetta CASP	Lab 2
Jan 31	Loop modeling	Ab initio: MODELLER Database search: FREAD Loop classification: Loop BriX
Feb 5	Template-based modeling	Fold prediction metaserver MODELLER and ModBase Literature: Sali & Blundell (MODELLER); Lathrop & Smith (threading)		Lab 2
Feb 7	Intro to protein design	pyRosetta workshop on protein design Kuhlman and Baker, PNAS 97:10383(2000)	SA 3
Feb 12	Algorithms of protein design		Lab 3	SA 3
Feb 14	Algorithms of protein design
Feb 19	Small-molecule docking	Papers: DOCK; AutoDock; AutoDock Vina Molecules: Zinc; DUDE Software: AutoDock Vina; AutoDock Tools; OpenBabel	Lab 4	Lab 3
Feb 21	Pharmacophores
Feb 26	Protein-protein docking	Literature: Gabb et al. (FTDock); Chen et al. (ZDock); Norel et al. (geom hashing) Sites: FT Dock; ZDock; CAPRI
Feb 28	Experimental structure determination			Lab 4
Mar 5	Paper discussion	Neil P. King et al., Computational Design of Self-Assembling Protein Nanomaterials with Atomic Level Accuracy, Science, 2012
Mar 7	Paper discussion	Lasker et al., "Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach", PNAS 2012