Wrap-and-Pack: A New Paradigm for Beta Structural Motif Recognition with Application to Recognizing Beta Trefoils
Speaker: Matt Menke , EECS/ CSAIL MIT
Date: March 10 2004
Time: 11:30AM to 12:45AM
Location: 2-338
Host: P Clote, BC & B Berger, MIT/ CSAIL
Contact: Kathleen Dickey, 617 253 3037, kvdickey@mit.edu
Relevant URL: http://www-math.mit.edu/compbiosem/**** Please note the special day of Wednesday & please excuse duplicate mailings ****
A method is presented that uses beta-strand interactions at both the
sequence and the atomic level, to predict the beta-structural motifs in
protein sequences. A program called Wrap-and-Pack implements this method, and is shown to recognize beta-trefoils, an important class of
globular beta-structures, in the Protein Data Bank with 92% specificity
and 92.3% sensitivity in cross-validation. It is demonstrated that Wrap-and-Pack learns each of the ten known SCOP beta-trefoil families, when trained primarily on beta-structures that are not beta-trefoils, together with 3D structures of known beta-trefoils from outside the family. Wrap-and-Pack also predicts many proteins of unknown structure to be beta-trefoils. The computational method used here may generalize to other beta-structures for which strand topology and profiles of residue accessibility are well conserved.
Refreshments: 11:00 am in the Applied Mathematics Common Room at MIT's Building 2, Room 349
The seminar is co-hosted by Professor Peter Clote of Boston College's Biology and Computer Science Departments and MIT Professor of Applied Math Bonnie Berger. Professor Berger is also affiliated with CSAIL & HST.
MIT
Department of Mathematics
& The Theory of
Computation Group
At CSAIL
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