DIMACS Workshop on Information Processing by Protein Structures in Molecular Recognition

Dates: June 13 - 14, 2005
DIMACS Center, CoRE Building, Rutgers University

Bhaskar DasGupta, University of Illinois at Chicago, dasgupta@cs.uic.edu
Jie Liang, University of Illinois at Chicago, jliang@uic.edu
Presented under the auspices of the DIMACS/BioMaPS/MB Center Special Focus on Information Processing in Biology.

This special focus is jointly sponsored by the Center for Discrete Mathematics and Theoretical Computer Science (DIMACS), the Biological, Mathematical, and Physical Sciences Interfaces Institute for Quantitative Biology (BioMaPS), and the Rutgers Center for Molecular Biophysics and Biophysical Chemistry (MB Center).

Workshop Program:

Monday, June 13, 2005

  8:15 -  8:50  Breakfast and registration

  8:50 -  9:00  Welcome and Opening Remarks
                Fred Roberts, DIMACS Director

  9:00 - 10:00  Protein-Protein Interfaces
                Johannes Rudolph, Duke University 

 10:00 - 10:20  Break

 10:20 - 11:20  Functional Annotation of Proteins with Known Structure by Structure and
                Sequence Similarity, DNA-protein Interaction Patterns and GO Framework
                Ilya N. Shindyalov, University of California at San Diego

 11:20 - 11:45  Algorithms for Structural Comparison and Statistical 
                Analysis of Three Dimensional Protein Motifs
                Brian Chen, Rice University 

 11:45 - 12:10  Reverse Engineering of Protein and Gene Networks: 
                how to design experiments efficiently? 
                Bhaskar DasGupta, UIC

 12:10 - 12:35  Computational mapping of proteins for exploring the role of binding 
                site plasticity in molecular recognition and information transfer
                Sandor Vajda, Boston University

 12:35 -  2:00  Lunch 

  2:00 - 2:50   Reconstructing a Circular Order from Inaccurate Adjacency
                Information with Applications in NMR Data Interpretation
                Ming-Yang Kao, Northwestern University 

  2:50 - 3:20   Break

  3:20 - 4:10   Novel Sequential Monte Carlo Techniques and Their Applications
                to Protein  Structure Analysis
                Jun Liu, Harvard University 

  4:10 - 4:35   Protein-protein Docking Algorithm Development and Testing
                Zhiping Weng, Boston University
  4:35 - 5:00   Using Unit Quaternion to Update Molecular Conformation
                V. Choi, X. Yu and W. Zheng 

  5:00 - 5:25   An approach to semi flexible docking: a case study of the enzymatic 
                reaction catalyzed by terpenoid cyclases
                Vladimir Sobolev, Weizmann Institute of Science, Israel 
  6:00          Dinner (DIMACS lounge)

Tuesday, June 14, 2005

  8:30 -  9:00  Breakfast and registration

  9:00 - 10:00  Modeling the chemosensing system of E. coli
                Ned Wingreen, Princeton University 

 10:00 - 10:20  Break

 10:20 - 11:10  On global optimization of the Lennard-Jones potential functions
                Claudio Cifarelli,  University of Rome "La Sapienza"
 11:10 - 12:00  Digital biology: Relations between data-mining
		in biological sequences and physical chemistry
                L. Ridgway Scott, University of Chicago 

 12:00 - 12:20  Fast and Accurate Protein Side-Chain Packing
                Jinbo Xu, MIT 

 12:20 - 12:40  Computational identification of binding sites in proteins
		Drena Dobbs, Iowa State University

 12:40 - 2:00   Lunch 

  2:00 - 2:50   Predicting protein interactions and their interfaces
                Mona Singh, Princeton University

  2:50 - 3:15   Break

  3:15 - 4:05   Multi-Scale Structure Prediction of Helical Transmembrane 
                Ying Xu, University of Georgia 

  4:05 - 4:20   Characterizations of protein functions through evolutionary
                models of structural binding surfaces
                Jie Liang, UIC

  4:20 - 4:35   Sequence order independent structural alignment
		Joe Dundas, UIC

  4:35 - 5:00   Consistent sets of secondary structures in proteins
                Jieun Jeong, Pennsylvania State University

  5:00 - 5:25   High throughput processing of the structural information of the 
                Protein Data Bank
                Zoltan Szabadka, Eotvos University, Hungary 

Previous: Participation
Next: Registration
Workshop Index
DIMACS Homepage
Contacting the Center
Document last modified on May 31, 2005.