Modeling and predicting the structure of transmembrane proteins
Speaker: Jerome Waldispuhl , Ecole Polytechnique & BC
Date: March 7 2005
Time: 11:30AM to 1:00PM
Location: 32-G575
Host: P Clote/ BC & B Berger/ MIT
Contact: Kathleen Dickey, 617 253-3037, kvdickey@mit.edu
Relevant URL: http://www-math.mit.edu/compbiosem/Modeling and predicting the structure of proteins is an important challenge of
computational biology. Exact physical models are too complex to be used without
approximations as prediction tools and most ab-initio methods only use local
information to fold a given sequence.
We show that transmembrane protein structure can be modeled with a multi-tape
S-attributed grammar. An efficient structure prediction algorithm using both
local and global constraints is designed, compiled by our system and
evaluated. Comparison with existing methods shows that the prediction rates as
well as the definition level are increased or equivalent on 124 known
structures of 80 to 600 residues. The accuracy of distinguishing globular from
membrane proteins has been evaluated with success on a dataset of 567
sequences. We are able to deal with both alpha-bundles and beta-barrels for the
first time. Furthermore, the model we propose is very versatile and can be
easily augmented with new features. It should be emphasized that the global
structure prediction in its principles does not depend on machine learning
methods.
Department of Mathematics
& The Theory of
Computation Group
At CSAIL
See other events that are part of Bioinformatics Seminar Series 2004/2005
See other events happening in March 2005
