Algorithms for Structure and Motion in Biology

Serafim Batzoglou & Jean-Claude Latombe

    Molecular biology is an exciting application area of computer science, because it presents new computational challenges that ultimately advance the field. Proteins, for example, are long macromolecules that can be modeled as chains in three dimensions with rotational degrees of freedom, a given surface area, and kinematic properties. In that respect, computational methods from robot arm movement, computational geometry, and dynamic simulations, are relevant to the modeling of proteins. However, proteins are vastly more complicated than typical robot arms, and have a complex surface that interacts with the environment. Traditional computational methods have to be modified, or give way to new techniques that are appropriate for the novel challenges of modeling proteins.

    This course will cover algorithms for modeling structure and motion in biology. It is a course about exciting new algorithms that are motivated by the challenges we face in modeling macromolecules and predicting their properties in silico. We will cover biology concepts as needed to present the algorithmic material in context. As this is a relatively new field, many of the methods are currently in development, and the structure of the course will reflect that fact. The main reading material will be papers from recent literature, the powerpoint slides, and lecture notes that the students scribe during the class. Coursework will consist of scribing lectures and a project that will involve programming and use of existing software.



Mon & Wed 11:00am - 12:15pm


Skilling 191


To contact the teaching staff, send e-mail to cs273-spr0506-staff@lists.stanford.edu.