Talk 1: HYBRID DATA MINING MODELING APPROACHES FOR THE ANALYSIS OF HIV-1 PROTEASE CRYSTAL STRUCTURES Talk 2: RHEOLOGICAL STUDY OF A SIMULATED POLYMERIC GEL: SHEAR BANDING
TITLE:
Talk 1: HYBRID DATA MINING MODELING APPROACHES FOR THE ANALYSIS OF HIV-1 PROTEASE CRYSTAL STRUCTURES
Talk 2: RHEOLOGICAL STUDY OF A SIMULATED POLYMERIC GEL: SHEAR BANDING
DATE:
Friday, April 2nd, 2010
TIME:
3:30 PM
LOCATION:
GMCS 214
SPEAKER:
Speaker 1 : Gene M. Ko, PhD Student, CSRC
Speaker 2 : Joris Billen, PhD Student, CSRC
ABSTRACT:
Abstract 1: A classification model to correlate 70 HIV-1 protease crystal structure binding pockets to one of its complexed FDA approved protease inhibitors in terms of their structural descriptors utilizing a hybrid data mining modeling approach has been developed. 456 chemical descriptors have been derived from the binding pocket structure of each crystal structure. Two hybrid approaches were developed, Random Forest-Linear Discriminant Analysis (RF-LDA) and Random Forest-Logistic Regression (RF-LR). Random Forest is used as a feature selection proxy, selecting for the most relevant descriptors used to train its classification model. The top ranked descriptors are then used to train the subsequent LDA and LR models. The classification performance of LDA and LR are compared against the Random Forest classifier used to perform the feature selection. As a model validation step, hierarchical clustering of the top ranked descriptors is performed to verify the descriptor selection by Random Forest can group together the binding pocket structures based on their complexed ligands. Analysis of the top ranked chemical descriptors would play a crucial role in understanding the HIV-1 protease binding pocket in terms of its chemical descriptors.
Abstract 2: In this talk simulations of polymeric gels (PG) are introduced. PG are used in several fields ranging from medical applications to consumer products (spandex, toothpaste, etc). For processing purposes it is important to understand the flow properties of the PG. They show Newtonian behavior at low shear rate, followed by a non-Newtonian shear thinning regime. In this non-Newtonian regime, experiments as well as simulations show shear banding; two bands with different shear rate exist. Simulations allow us to gain understanding of this phenomenon on the microscopic level.
HOST:
Sunil Kumar and Arlette Baljon
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