DIMACS Workshop on Information Processing by Protein Structures in Molecular Recognition

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

Organizers:

Bhaskar DasGupta, University of Illinois at Chicago, dasgupta@cs.uic.edu

Jie Liang, University of Illinois at Chicago, jliang@uic.edu

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).

Abstracts:

• Piotr Berman and Jieun Jeong, Pennsylvania State University
  Predicting Secondary Structures of Protein and Global Optimization

• Brian Y. Chen, Viacheslav Y. Fofanov, David M. Kristensen, Marek Kimmel,
  Olivier Lichtarge, and Lydia E. Kavraki, Rice University
  Algorithms for Structural Comparison and Statistical Analysis of 3D Protein Motifs

• Zhong Chen and Ying Xu, University of Georgia
  Multi-Scale Hierarchical Structure Prediction of Helical Transmembrane Proteins

• Vicky Choi, Virginia Tech
  On Updating Torsion Angles of Molecular Conformations

• Karl H. Clodfelter and Sandor Vajda, Boston University
  Computational Mapping of Proteins for Exploring the Role of Binding Site Plasticity in
  Molecular Recognition and Information Transfer

• Bhaskar DasGupta, UIC
  Randomized Approximation Algorithms for Set Multicover Problems
  with Applications to Reverse Engineering of Protein and Gene Networks

• Joe Dundas, Andrew Binkowski, Bhaskar DasGupta, Jie Liang, University of Illinois at Chicago
  Sequence Order Independent Structural Alignment

• Ming-Yang Kao, Northwestern University
  Reconstructing a Circular Order from Inaccurate Adjacency Information

• Jie Liang, UIC
  Inferring Protein Functions by Matching Binding Surfaces through Evolutionary Models

• L. Ridgway Scott, University of Chicago
  Digital biology: Relations between Data-mining
  in Biological Sequences and Physical Chemistry

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

• Vladimir Sobolev, Weizmann Institute of Science, Israel
  An Approach to Semi Flexible Docking: a Case Study of the Enzymatic
  Reaction Catalyzed by Terpenoid Cyclases

• Zoltan Szabadka, Eotvos University, Hungary
  High Throughput Processing of the Structural Information of the
  Protein Data Bank

• Ned Wingreen, Juan Keymer, Robert Endres, Princeton University and
  Yigal Meir, Ben Gurion University
  Modeling the Chemosensing System of E. coli

• Jinbo Xu, MIT
  Rapid Protein Side-Chain Packing via Tree Decomposition

• Jinfeng Zhang, Harvard University
  Protein Structure Analysis with Sequential Monte Carlo Method

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