Seminar by Thomas Hamelryck

Wednesday October 23 at 3.15 pm in aud 10 (HCØ, Universitetsparken 5, 2100 København Ø). Tea and chocolate will be served in room 04.3.15 after the seminar.

Title: Probabilistic models of protein structure
Thomas Hamelryck, The Bioinformatics Centre, UCPH

ABSTRACT: The so-called protein folding problem is the loose designation for an amalgam of closely related, unsolved problems that include protein structure prediction, protein design and the simulation of the protein folding process. We adopt a unique probabilistic approach to modeling bio-molecular structure, based on graphical models, directional statistics and probability kinematics. Notably, we developed a generative probabilistic model of protein structure in full atomic detail. I will give an overview of how rigorous probabilistic models of something as complicated as a protein's atomic structure can be formulated, focusing on the use of graphical models and directional statistics to model angular degrees of freedom. I will also discuss the reference ratio method, which is needed to "glue" several probabilistic models of protein structure together in a consistent way. The reference ratio method is based on "probability kinematics", a little known alternative to Bayesian updating proposed by the philosopher Richard C. Jeffrey at the end of the 50ies. Probability kinematics might find widespread application in statistics and machine learning as a way to formulate complex, high dimensional probabilistic models by combining several simple models.