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 | ||
March | 30 | JP | Protein bioinformatics 1: access to information | ||||
April | 1 | JP | Protein bioinformatics 2: evolution | ||||
April | 6 | SP | Physical properties of amino acids | ||||
April | 8 | SP | Protein structure essentials → updated handout | ||||
April | 13 | SP | How to visualize proteins → a Cn3D Mac plugin is here | ||||
April | 15 | SP | Why proteins fold | ||||
April | 20 | SP | Structure determination and databases | ||||
April | 22 | SP | Crystallography practicum | ||||
April | 27 | BC | Quantitative proteomics | ||||
April | 29 | GB | Proteomics and systems biology [ AT_pH5.tab | AT_pH7.tab | AT_pH7_5.tab ] overview.jpg ] | ||||
May | 4 | IR | Protein structure data bases and classification | ||||
May | 6 | IR | More on data bases and classification; Protein secondary structure prediction | ||||
May | 11 | IR | Protein tertiary structure prediction | ||||
May | 13 | IR | Protein structure prediction (CASP) | ||||
May | 18 | Review; New: iTraq figure and example | |||||
May | 20 | Final exam |