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 various guest lecturers.

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 W2033. Labs are every other Friday, 2.00-3.20pm, in W3017.

N: Notes H: Homework L: Links and Handouts I: Instructor

Date		N	H	L	I	Topic
March	25				SP	Introduction to physical properties of amino acids
	27				SP	Introduction to protein structure
April	1				SP	Protein structure determination
	3				SP/IR	Entropy, enthalpy, free energy, folding, algorithms
	8				IR	Protein structure: data bases and classification
	10				IR	More on data bases and classification; secondary structure prediction
	11				SP	Lab @ noon in W3017
	15				IR	Protein tertiary structure prediction
	17				IR	Protein structure prediction, CASP
	18				IR	Lab @ 1pm in W3017
	22				JP	Protein bioinformatics (1)
	24				JP	Protein bioinformatics (2)
	29				JG	Cancelled (old slides available via link)
May	1				RC	Applications of mass spectrometry to proteomics
	6				BC	Quantitative proteomics
	8				RC	Protein data bases for mass spectrometry analysis
	9					Lab
	13					Review
	15					Final exam