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
Structural
Bioinformatics. Wiley, Bourne Weissig, Eds.
Course Information
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Lectures: T,TH; 12:00 - 1:20; WeH 4615A
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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 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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Introduction
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Overview and Motivation
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Fundamentals of amino acids
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Chs. 1,2
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Protein Structure and Folding
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Ch. 17
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Protein Data Bank and Visualization
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Ch. 7-9
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#1 handed out
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Geometry and Kinematics
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Experimental Methods
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XRC 1
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Ch. 4
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XRC 2
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NMR 1
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Ch. 5
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NMR 2
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#1 due, #2 handed out
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CryoEm and other techniques
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Ch. 6
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Evaluating Structures
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Chs. 14,15
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Analysis and Prediction
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Comparing Structures
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Ch. 16
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Mining Structures
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Ch. 11
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#2 due, #3 handed out
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Structural Domains
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Ch. 18
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CATH and SCOP
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Chs. 12,13
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Structure and Function
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Ch. 19
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2ndary and super-secondary structure prediction
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Ch 28.
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Threading
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Ch. 26
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#3 due, #4 handed out
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Homology Modeling
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Ch. 25
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Ab initio prediction and CASP
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Ch. 24,27
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No class, holiday
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Applications
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Protein Interactions
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Chs. 20,21
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Docking and Drug Design
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Ch. 22,23
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#4 due
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Molecular Dynamics
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Protein-redesign
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