Structural Bioinformatics
I619 - Spring 2008
class ID: 28329
▪ Syllabus
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Week 1: January 7-11, 2008
Topics
Overview of the course
What is structural bioinformatics?
The logic of biological phenomena.
Reading material
Textbook: Defining bioinformatics and structural bioinformatics (chapter 1)
Week 2: January 14-18, 2008
Topics
Fundamentals of protein structure
Protein folding and function
Reading material
Textbook: Fundamentals of protein structure (chapter 2)
Branden and Tooze: The building blocks (chapter 1)
Branden and Tooze: Motifs of protein structure (chapter 2)
Branden and Tooze: Folding and flexibility (chapter 6)
(Lecture slides Mon) (Lecture slides Wed) (Anfinsen's experiment)
Week 3: January 21-25, 2008
Topics
Fundamentals of DNA structure
Reading material
Understanding DNA by Calladine et al. (chapters 1-4)
Week 4: January 28-February 1, 2008
Topics
Protein structure determination:
Circular dichroism (CD) spectroscopy
Coiled-coil proteins
Reading material
Branden and Tooze: Fibrous proteins (chapter 14)
Guest Lecturer
Prof. Vladimir Uversky, School of Medicine
Vincent Waldman, Department of Chemistry
(Lecture slides Mon) (Lecture slides Wed) (Homework assignment #1) - due Feb. 11 in class
Week 5: February 4-8, 2008
Topics
Protein structure determination:
X-ray Crystallography
NMR spectroscopy
Interpreting/understanding structural data
Reading material
Textbook: Computational aspects of high-throughput crystallographic macromolecular structure determination (chapter 4)
Textbook: Macromolecular structure determination by NMR spectroscopy (chapter 5)
Textbook: Structural quality assurance (chapter 14)
Useful web resource
Joseph Hornak's (Rochester Institute of Technology) introduction to NMR.
Gale Rhodes' (University of Southern Maine) glossary of experimental terms.
Crystallography and Crystallographic Information (UIUC) here
(Lecture slides Mon) (Lecture slides Wed) (Homework assignment #2)
Week 6: February 11-15, 2008
Topics
Understanding sequence-structure-function relationship
Structure databases: Structural Classification of Proteins (SCOP)
Structure databases: CATH classification (CATH)
Reading material
Textbook: Protein structure evolution and the SCOP database (chapter 12)
Textbook: The CATH domain structure database (chapter 13)
(Lecture slides Mon) (Homework assignment #3) - due Feb. 27 in class (presenter Wyatt Clark)
Week 7: February 18-22, 2008
Topics
Protein domains
Prediction from 3-D structure
Prediction from amino acid sequence only
Reading material
Textbook: Identifying structural domains in proteins (chapter 18)
(Lecture slides Mon) (Lecture slides Wed) (Homework assignment #4) - due March 17 in class (presenter Dah Mee Ko)
Week 8: February 25-29, 2008
Topics
Automated assignment of secondary structure (DSSP)
Structural similarity measures
Reading material
Textbook: Secondary structure assignment (chapter 17)
Useful reading
W. Kabsch, C. Sander. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers (1983) 22:2577-2637.
(Lecture slides Mon) (Lecture slides Wed) (Homework assignment #5) - due March 19 in class (presenter Yong Li)
Week 9: March 3-7, 2008
Topics
Molecular visualization
Midterm Exam
Reading material
Textbook: Identifying structural domains in proteins (chapter 18)
(Homework assignment #6) - due March 26 in class (presenter Jun Ma)
Week 10: March 10-14, 2008
Spring Break
Week 11: March 17-21, 2008
Topics
Structure alignment
Combinatorial extension algorithm (CE)
Statistical learning: classification techniques
K nearest neighbor method
Logistic regression
Recommended reading
I. N. Shindyalov, P.E. Bourne. Protein structure alignment by incremental combinatorial extension of the optimum path. Protein Engineering (1998) 11(9) 739-747.
(Lecture Slides Mon) (Lecture Slides Wed) (Homework assignment #7) - due March 31 in class (presenter Mauli Prasad)
Week 12: March 24-28, 2008
Topics
Neural networks
Prediction of protein features from sequence
Prediction of secondary structure
Prediction of protein disorder
(Lecture Slides from Tom Mitchell's book on Machine
Learning - ch. 4) (Homework
assignment #8) - due April 7 in class (presenter Arunima Ram)
Week 13: March 31-April 4, 2008
Topics
Prediction of protein features from sequence
Prediction of secondary structure
Prediction of protein disorder
Guest lecture on Wednesday: Sean Mooney, Structural characterization of proteins using residue environments. Lab web site.
(Lecture Slides Mon) (Homework
assignment #9) - due April 9 in class (presented Sriram Raghuraman)
Week 14:
April 7 - 11, 2008
Topics
Prediction of protein 3D structure
Docking methods
(Homework
assignment #10) - due April 9 in class (presenter Nils Schimmelmann)
(Homework
assignment #11) - due April 14 in class (presenter Dan Schrider)
Last updated: 04/06/2008 07:31 PM