Events - Colloquia & Seminars

CCIS Colloquium Spring 2006

Algorithmic Challenges and Biological Results in Computational and Systems Biology

Speaker: Ryan Lilien

Host: Jay Aslam

Date: Friday, March 24, 2006

Talk: 12:00 pm, 366 WVH

Abstract

With the recent completion of the human genome project researchers are racing to determine the correlations between genomic sequence and protein expression, the structures and functions of these proteins and protein systems, and the molecular derangements present in disease. This talk will discuss several of our recent projects in Computational and Systems Biology including the development of efficient algorithms for (1) modeling of molecular flexibility using molecular ensembles for drug design and protein redesign (K*), (2) analysis of mass spectrometry proteomics data of human blood sera for disease diagnosis (Q5), and (3) extending data analysis for structural biology and macromolecular structure determination. We will focus on the first of these projects: We developed a novel algorithm for protein redesign, which combines a statistical mechanics-derived ensemble-based approach to computing the binding constant with the speed and completeness of a branch-and-bound pruning algorithm. In addition, we show that the state-of-the-art dead-end elimination (DEE) pruning criteria for identifying low-energy conformations can not be used directly in computing partition functions with energy minimization. We therefore extend the DEE framework to allow DEE to be incorporated into a hybrid ensemble-based mutation search incorporating DEE, A* search, and our ensemble-based scoring function K*.

Note: If you understand that, at a high-level, atoms come together to form molecules, then you have the necessary chemical and biological background for this talk.