Computer Science 663
Algorithms in Structural Biology

Spring, 2013

Time: 10:05 - 11:20 pm Monday and Wednesday
Place: LSRC A155

Professor: Bruce Randall Donald
TA: Jonathan Jou
TA Office Hours: LSRC D301 Tuesday, 5 PM - 6 PM, Thursday, 3:30 PM - 4:30 PM

This course is cross-listed as CBB 663.

This webpage is under construction. In particular, the syllabus, schedule, and topics pages are not final, but they give an idea.

Overview | Course Mechanics, and Textbooks | Schedule | Topics | How to give a good talk
Assignments | Supplemental Materials | Some Relevant WWW Links


Introduction to algorithmic and computational issues in structural molecular biology and molecular biophysics. Emphasizes geometric algorithms, provable approximation algorithms, computational biophysics, molecular interactions, computational structural biology, proteomics, rational drug design, and protein design. Explores computational methods for discovering new pharmaceuticals, NMR and X-ray data, and protein-ligand docking.

This course focuses on computational structural biology. We will emphasize themes that unite algorithms, modelling, and experimental results. Topics will include algorithms, modeling, and experimental validation for several areas of biophysics including NMR, protein design, x-ray crystallography, structural immunology, and structure-based drug design. Students should have (or be willing to learn) a grasp of basic structural biochemistry and have a familiarity with algorithms. However, students with a strong background in One of these areas may, with permission of the instructor, take the course if they are prepared to do some extra reading. It is helpful to have a basic knowledge of algorithm design, or probability and statistics, or molecular biology, and computer programming. Graduate and undergraduate students are welcome.

There will be lectures by the instructor. In addition, students will do a project, will present research papers from the literature, and also write and edit notes on these papers.

The Textbook for this class is: Algorithms in Structural Molecular Biology (MIT Press, 2011), also available on Amazon.

Molecular Visualization Software for this class

Textbooks for this course