Instructor: Christopher James Langmead, Department of Computer Science, Carnegie Mellon University


Textbook (optional): Molecular Modeling and Simulation: An Interdisciplinary Guide. Tamar Schlick

Lectures: Tuesdays and Thursdays 12-1:20, GHC 4101, CMU

Discussion Group

Syllabus

Date	Module	Topic	Slides and Reading	Assignment
1/12	Introduction	Challenges and History of Structural Biology	slides
1/14	Background	Physics and Chemistry	background slides
1/19		Amino Acids and Proteins	slides, supplemental notes
1/21		Internal vs Free Energy	slides
1/26		Structure Determination: XRC, NMR, CryoEM	slides	1st assignment
1/28	Static Analysis and Modeling	Force Fields and Fast Electrostatic Calculations	slides
2/2		Elastic Network Models	slides ANM mass-spring1 mass-spring2
2/4		Multivariate Optimization	slides, superposition
2/9		Snow Day!!!
2/11		Structural Bioinformatics; Rigid Aligment	slides
2/16		Ab initio structure prediction	slides	1st assignment due
2/18		Fast Electrostatics (part 2)	slides PME paper FMM tutorial
2/23		Algebraic Geometry	slides
2/25		Structure Comparison and Alignment	slides
3/2		Homology Modeling	slides	2nd assignment
3/4		Threading	slides
3/9		no class, Spring Break
3/11		no class, Spring Break
3/16		Graphical Models 1	slides
3/18		Graphical Models 2	slides	2nd assignment due
3/23		Graphical Models 3	slides
3/25		Protein Design	slides
3/30		Drug Design	slides
4/1	Dynamic Modeling and Analysis	Molecular Dynamics	slides	3rd assignment
4/6		Monte Carlo	slides
4/8		Analyzing MD Data; Free Energy Calculations	slides
4/13		Coarse Grained Simulation 1	slides
4/15		no class, Carnival
4/20		Coarse Grained Simulation 2	slides
4/22		Multiscale;Distributed Computing	slides
4/27		Class presentations
4/29		Class presentations		3rd assignment due