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).
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
Proteins
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
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