[Colloquium] REMINDER: Thesis Defense tomorrow at 1:30-Feng Zhao

[Dawn Ellis]

When:     Friday, October 25th, 2013 at 1:30pm

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

Who:       Feng Zhao

Title:       Structural Learning for Template-free Protein Folding

Abstract:

My thesis is aimed to solve the template-free protein folding problem by
tackling two important components: efficient sampling in vast conformation
space, and design of knowledge-based potentials with high accuracy. In my
talk, I will introduce a series of statistical machine learning methods to
efficiently lead the folding process from primary sequences. The
first-order and second-order Conditional Random Fields models are applied
to sample structures from the continuous local dihedral angles space by
modeling the lower and higher order conditional dependency between
neighboring dihedral angles given the primary sequence information. A
framework combining CRF and the energy function is introduced to guide the
local conformation sampling using long range constraints with the energy
function. The relationship between the sequence profile and the local
dihedral angle distribution is nonlinear. Hence we proposed the CNF-Folder
to model this complex relationship by applying a novel machine learning
model Conditional Neural Fields which utilizes the structural graphical
model with the neural network. CRF-Samplers and CNF-Folder perform very
well in CASP8 and CASP9. Further, a novel pairwise distance statistical
potential (EPAD) is designed to capture the dependency of the energy
profile on the positions of the interacting amino acids as well as the
types of those amino acids, opposing the common assumption that this energy
profile depends only on the types of amino acids. EPAD has also been
successfully applied in the CASP 10 Free Modeling experiment with
CNF-Folder, especially outstanding on some uncommon structured targets.

***Feng's thesis will be accessible in hard copy in the 5th floor commons
area.*

Thesis Advisor: Prof. Jinbo Xu

-- 
*Dawn Ellis*
Administrative Coordinator,
Bookkeeper
773-834-1757
dellis at ttic.edu

TTIC
6045 S. Kenwood Ave.
Chicago, IL. 60637
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