EECS 800 Protein Bioinformatics

Instructor	Text Book	Grades
Course Description	Exam	Lectures
Prerequisites	Project	Useful Links

Instructor

Dr. Xue-wen Chen

Ø Phone: (785)864-8825

Ø Email: xwchen AT ku DOT edu

Ø Office: Eaton 2028

Ø Lectures: TTH, 2:30 am – 3:45 am

Ø Location: Room 2111 Learned Hall

Ø Class Number: 65512

Ø Office Hours: TTH: 3:45 pm – 5:45 pm or by appointment

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Course Description

This course emphasizes the applications of computational algorithms to main problems in protein bioinformatics and molecular biology. A variety of topics, including protein sequence alignments, profiles, and protein structure classification and prediction, will be either introduced briefly or discussed in detail. Background in molecular biology will also be introduced briefly. Students may be asked to present some selected research papers (as groups).

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Prerequisites

Ø Probability and statistics (EECS 461).

Ø Some experience with computer programming (MATLAB or C or C++).

Ø An introductory course in biology will be helpful but not essential.

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Text Book

Ø Ingvar Eidhammer, Inge Jonassen, and William Taylor, Protein Bioinformatics: An Algorithm Approach to Sequence and Structure Analysis, 2004, ISBN 0470848391, John Wiley & Sons, Ltd.

Ø Author Lesk, Introduction to Protein Architecture, 2001, ISBN: 0198504748, Oxford University Press

Ø Additional handouts will be provided in class as required.

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Exam

Ø No exam.

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Project

Students will form groups to complete a course project. Each group consists of 2 ~ 3 students and chooses a topic that pertains to the course material.

Each group should be formed and submit a pre-proposal. The pre-proposal should describe the project goal, the problems to be studied, current methods, proposed methods, expected results, references, names of the group members and responsibilities of each member (about 5 pages: single space, fond size = 12, references are not counted).

In addition to the issues addressed in pre-proposal, the final project should include your results and discussions. A written final report in the style of a journal article is also required.

Each group will give classroom presentation about the final project.

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Grades

Course grade will be assigned based on scores on programming assignments, pre-proposal, final project, and presentation. The final grade is made up of the following:

Ø Assignments: 30%

Ø Pre-proposal: 15%

Ø Final Project: 40%

Ø Presentation 15%

The cutoffs for grades will be roughly as follows:

A: 90 – 100 B: 80 – 89 C: 70 – 79 D: 60 – 69 F: 0 – 59

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Lectures

Ø Introduction to Protein Bioinformatics

Ø Introduction to Molecular Biology

Ø In vivo, in vitro, in silicio

Ø Pattern and form in protein structure

Ø The varieties of protein structure

Ø Pairwise sequence alignment

Ø Multiple sequence alignment

Ø Phylogenetic trees

Ø Profiles

Ø Structure and structure descriptions

Ø Protein structure comparison

Ø Protein structure classification

Ø Threading

Ø Protein-protein Interaction

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Useful Links

Ø NCBI BLAST (about sequence alignment)

Ø BLAST PROGRAMS (list of BLAST programs)

Ø MSA CLUSTALW (Multiple Sequence Alignment)

Ø HMMER (profiles HMMs for protein sequence analysis)

Ø PDB (Protein Data Bank)

Ø UNIPROT (Universal Protein Resource)

Ø ExPASy (Expert Protein Analysis System)

Ø PROSITE (database of protein families and domains)

Ø SWISS-2DPAGE (2D Polyacrylamide gel electrophoresis database)

Ø CATH (Class-Architecture-Topology-Homologe)

Ø SCOP (Structural Classification of Proteins)

Ø ASTRAL (databases and tools for protein structure/sequence analysis)

Ø Pfam (protein domains)

Ø InterPro (a database of protein families, domains and functional sites)

Ø MIPS (PPI databases, links to other PPI dbs, e.g, DIP, BIND etc.)

Ø CASP (Check it out! Critical Assessment of Techniques for Protein Structure Prediction)

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