Description:
Provides students with an overview of protein bioinformatics including computational and experimental approaches. The course 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:
Joel Bader (JB), Robert Cotter (RC), Jeff Gray (JG), Akhilesh Pandey (AP), Jonathan Pevsner (JP), Sean Prigge (SP), Ingo Ruczinski (IR), Heng Zhu (HZ).

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

Time and Place:
T-Th 3-4:20, SPH W2033.

2: Notes (2 slides per page) 6: Notes (6 slides per page) H: Homework L: Links and Supplements I: Instructor

Date		2	6	H	L	I	Topic
March	29					SP	Introduction to physical properties of amino acids
	31					SP	Protein structure (level of Branden and Tooze)
April	5					JP	Protein sequence alignment and evolution
	7					RC	Principles of mass spectrometry
	12					AP	Applications of mass spectrometry to proteomics
	14					AP	Applications of mass spectrometry to proteomics
	19					SP	Protein structure determination
	21					IR	Protein databases, structural classification of proteins, visualization
	26					IR	Protein secondary structure prediction
	28					IR	Protein structure prediction
May	3					IR	Protein structure prediction
	5					JB	Protein networks
	10					HZ	High throughput approaches to proteomics
	12					JG	Protein-protein docking
	17						Lab
	19						Final