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)

 

(Lecture slides Mon)


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)

 

(Lecture slides Wed)


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

 

(Lecture Slides Mon)

(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