Computational Structural Biology 15-879(A)
Instructor
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Chris Langmead, WeH 4103, cjl at cs.cmu.edu
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Description
Some of the most interesting and difficult challenges in computational
biology and bioinformatics arise from the determination, manipulation, or
exploitation of protein structures. This course will survey these challenges
and present a variety of computational methods for addressing them. The
course is appropriate for both students with backgrounds in computer science
and those in the life sciences.
Prerequisites
Programming Experience
Textbook
Molecular Modeling and Simulation: An Interdisciplinary Guide. Tamar Schlick
Course Information
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Lectures: T,TH; 12:00 - 1:20; WeH 5409
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Office Hours: by appointment
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Class Wiki; The
Wiki will be the primary means of distributing materials, including lecture notes, homework specifications
and various policies regarding grades.
Syllabus
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Date
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Unit
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Topic
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Reading
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Assignment
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1/16
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Introduction
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Overview; History of Structural Biology
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Ch 1
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1/18
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Review
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Biology
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1/23
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Chemistry
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1/25
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Amino acids and proteins
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Ch 2,3
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1/30
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Free Energy; Folding; Molecular Mechanics
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2/1
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Modeling and Analysis
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Techniques for Multivariate Non-linear Optimization
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2/6
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Fast Electrostatic Computations
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Ch 21
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2/8
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X-ray Crystallography 1
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Ch 4
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2/13
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X-ray Crystallography 2
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1st assignment goes out
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2/15
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Nuclear Magnetic Resonance
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Ch 5
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2/20
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Structure Comparison and Mining 1
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Chs 6-16
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2/22
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Guest Lecture: Hetunandan Kamisetty; All atom modeling
using
probabilistic graphical models
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Handout
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2/27
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Structure Comparison and Mining 2
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Chs 6-16
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3/1
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Modeling Flexibility
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2nd assignment goes out
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3/6
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Side-chain placement; Dead-end elimination
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3/8
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Homology Modeling
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Ch 24,25
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Term project proposal due
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3/13
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Spring break
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3/15
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Spring break
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3/20
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Threading
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Ch 26
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3/22
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Simulation
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Ab initio
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Ch 27
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3/27
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MCMC, Annealed importance sampling
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3/29
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Guest lecture: Dan Zuckerman
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4/3
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Milestoning
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3rd homework goes out; Wikipedia entry proposal due
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4/5
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HP and Go models
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4/10
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Formal Methods
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Handout
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4/12
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Guest Lecture: Lillian Chong
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4/17
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Docking and Drug design
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Chs 22, 23
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4/19
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Protein design
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4/24
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No class
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4/26
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Presentations
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5/1
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Presentations
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5/3
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No class
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