[Colloquium] 1/20 Research at TTIC: Mark Hallen, TTIC

[Mary Marre via Colloquium]

When:     Friday, January 20th at noon



Where:    TTIC, 6045 S Kenwood Avenue, 5th Floor, Room 526



Who:       Mark Hallen; TTIC


Title:       CATS (Coordinates of Atoms by Taylor Series): A Powerful New
Model of Backbone Flexibility for Protein Design

Abstract:
Computational protein design algorithms search for modifications in protein
systems that will optimize a desired function.  Usually, this function
involves chemical binding of a protein to another protein or to a drug.
Binding is exquisitely sensitive to the 3-D geometry adopted by the system,
with low-energy geometries preferred, so to optimize binding we must be
able to optimize energy with respect to molecular geometry. The hardest
part of molecular geometry to model has generally been the protein
backbone, because we often seek significant local perturbations that do not
disturb the rest of the protein structure, and this leads to a set of
equality constraints that is difficult for previous algorithms to handle.

In this talk, I will first describe the paradigm for protein design used in
the OSPREY software package, in which we first build a model of protein
flexibility based on assigning allowed ranges to each internal coordinate,
and then optimize an approximation of the energy over that space with
provable guarantees of accuracy.  I will then describe how CATS builds on
this model, preserving its benefits while searching a much more realistic
space of backbone geometries.  By describing the backbone geometry with a
new set of internal coordinates, CATS allows the efficient energy
optimization methods in OSPREY to handle significant local perturbations
without disturbing the rest of the protein.



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*Research at TTIC Seminar Series*

TTIC is hosting a weekly seminar series presenting the research currently
underway at the Institute. Every week a different TTIC faculty member will
present their research.  The lectures are intended both for students
seeking research topics and adviser, and for the general TTIC and
University of Chicago communities interested in hearing what their
colleagues are up to.

To receive announcements about the seminar series, please subscribe to the
mailing list: https://groups.google.com/a/ttic.edu/group/talks/subscribe

Speaker details can be found at: http://www.ttic.edu/tticseminar.php.

For additional questions, please contact Nathan Srebro at nati at ttic.edu
<mcallester at ttic.edu>


Mary C. Marre
Administrative Assistant
*Toyota Technological Institute*
*6045 S. Kenwood Avenue*
*Room 504*
*Chicago, IL  60637*
*p:(773) 834-1757*
*f: (773) 357-6970*
*mmarre at ttic.edu <mmarre at ttic.edu>*
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