Protein Bioinformatics (260.655)

Course Description:
This course provides students with an overview of protein bioinformatics including computational and experimental approaches. It will introduce amino acid and protein physical properties as well as the alignment and evolution of protein sequences. Protein structure and methods of structure determination will be presented as well as the use of protein databases and software for visualizing proteins. Methods for secondary and tertiary protein structure prediction will be discussed as well as methods for modeling small/molecule-protein interactions and protein-protein interactions. The course will also cover mass spectrometry and the analysis of high-throughput mass spectrometry data. A survey of mass spectrometry ionization techniques and instrument types will be followed by an overview of data analysis techniques for protein identification, de novo protein sequencing, and the analysis of post-translational modifications. Finally, students will be introduced to experimental and computational aspects of mapping protein interaction networks.

Objectives:
The objective of the course is to provide students with the ability to analyze and understand data from high-throughput proteomics experiments. At the conclusion of the course the students will be able to (a) Define protein physical properties and analyze protein structure, (b) Explain how proteins are studied experimentally and how data is generated in high-throughput experiments, (c) Describe the computational methods used to study protein structure and interactions, (d) Explain the algorithms, statistical techniques and software tools used to analyze high-throughput proteomics data.

Intended audience:
Students enrolled in the MHS in Bioinformatics program as well as others interested in protein bioinformatics.

Instructors:
Jonathan Pevsner (JP), Sean Prigge (SP), Ingo Ruczinski (IR), with guest lecturers Bob Cole (BC) and Gundula Bosch (GB).

Prerequisites:
Introduction to Molecular Biology (120.602) or permission of the instructors.

Time and Place:
Lectures are Tuesday and Thursday, 3.30-4.50pm, in W4019.


NEW Here is the take-home part of the final, as a Word document and as a pdf.


Notes / Homework / Links and Handouts / Instructor



Date N H L I Topic
March30 JP Protein bioinformatics 1: access to information
April1 JP Protein bioinformatics 2: evolution
April6 SP Physical properties of amino acids
April8 SP Protein structure essentials → updated handout
April13 SP How to visualize proteins → a Cn3D Mac plugin is here
April15 SP Why proteins fold
April20 SP Structure determination and databases
April22 SP Crystallography practicum
April27 BC Quantitative proteomics
April29 GB Proteomics and systems biology [ AT_pH5.tab | AT_pH7.tab | AT_pH7_5.tab ] overview.jpg ]
May4 IR Protein structure data bases and classification
May6 IR More on data bases and classification; Protein secondary structure prediction
May11 IR Protein tertiary structure prediction
May13 IR Protein structure prediction (CASP)
May18 Review; New: iTraq figure and example
May20 Final exam