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The Department of Informatics and the Computational Biology Unit (CBU), in cooperation with the Research Group for Language Models and Resources (LaMoRe), invites to the following lecture:

December 3, 2007 at 14:15 in room HIB:LA/2142 (Høyteknologisenteret, datablokken)

Julia Hockenmaier (University of Illinois at Urbana-Champaign):


«We know that adult speakers of a language have no problem understanding newspapers in that language, and that proteins fold spontaneously into specific three-dimensional structures. However, a sentence in the Wall Street Journal may have millions of possible grammatical analyses, and a protein may have millions of possible structures. As computer scientists who want to design systems that can either parse natural language or predict the folded structure of proteins, we are faced with two very similar search problems: In both cases, we want to find the optimal structure of an input sequence among an exponential number of possible alternatives.

In this talk, I will demonstrate how CKY, a standard dynamic programming algorithm that is normally used in natural language parsing, can be adapted to give us novel insights into the protein folding problem. If we assume that folding is a greedy, hierarchical search for lowest-energy structures, CKY provides an efficient way to find all direct folding routes. I will also show that we can extend CKY to construct a Markov chain model of the entire folding process, and that this Markov chain may explain an apparent contradiction between what experimentalists observe in a test tube and what many theorists predict.

So far we have applied CKY only to simplified lattice models of proteins, and I will also use this talk to sketch how we can extend this approach to realistic representations of real proteins.»
(Proteinfolding og koplingen til formelle språk er forøvrig allerede dekket i Gödel, Escher & Bach.)

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