Computational structural biology aims to model and predict the structure of bio-molecules (e.g., proteins, DNA, RNA). This fields of study has a broad impact on the understanding of gene regulation processes and biological system mechanisms. It also open new research directions in synthetic biology such as the design of new bio-molecular devices and the re-engineering of biological functions.

The topics covered will range from the classic techniques in the field (e.g. molecular dynamics and hidden Markov models) to more recent advances in analyzing and predicting RNA and protein structure (e.g. conditional random fields tree grammars).

The class is intended for grad students interested in the application of mathematical and computational methods to molecular biology and also for biologists and biochemists interested in the algorithmic foundations of the approaches used in this field. Prerequisites: Basic understanding of algorithms. No biological background required. The class will provide background for any advanced methods discussed. The evaluation will consist of paper reviews and a final collective project.



Proteins: id picture

Image produced with RNAmovies

Course informations

Instructor: Jérôme Waldispühl

Lectures: Tuesday-Thursday 2:00pm - 3:30pm in McConnell 320.

Office hours: TBA.

Schedule and Material



Computational Molecular Biology: An Introduction
Peter Clote, Rolf Backofen
Wiley Series in Mathematical and Computational Biology


Notes have been released using material kindly provided by Peter Clote, Ivo Hofacker, David Mathews, Alain Laederach, Thomas Simonson and Jinbo Xu.