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Morning SessionApplications of Computational Geometry to Molecular Structure8:40 - 8:50 a.m.Introduction to Biogeometry: Applications of Computational Geometry to Molecular Structure view paper (.pdf)
8:50 - 9:10 a.m.Coarse and Reliable Geometric Alignment for Protein Dockingby Y. Wang, P.K. Agarwal, P. Brown, H. Edelsbrunner, and J. Rudolph (Duke) view paper (pdf) | presentation (ppt)
9:10 - 9:30 a.m.Computational Design of Combinatorial Peptide Library for Modulating Protein-Protein Interactionsby X. Li and J. Liang (UIC) view paper (pdf)
9:30 - 9:50 a.m.Exploring Protein Folding Trajectories Using Geometric Spanners by D. Russel and L. Guibas (Stanford) view paper (pdf)| presentation (ppt)
10:20 - 10:40 a.m.An Adaptive Dynamic Programming Algorithm for the Side Chain Placement Problem by A. Leaver-Fay, B. Kuhlman, and J. Snoeyink (UNC)
view paper (pdf)
10:40 - 11:00 a.m.ChainTweak: Sampling from the Neighbourhood of a Protein Conformation by R. Singh and B. Berger (MIT) view paper (pdf)
11:00 a.m. - 12:30 p.m.Biogeometry Discussion Session: What Could Experimental Biologists Learn from Computational Geometry Based Models of Biomolecules?
Afternoon Meeting 2:00 - 2:05 p.m.Introductionby Herbert Edelsbrunner (Duke)
2:05 - 2:20 p.m.Presentation (Protein-like Structures, Scoring Functions, Surface Geometry to Function) by Jie Liang (UIC)
PI Presentations 2:20 - 2:30 p.m.Presentation on work at Duke (Protein Docking, Protein Interfaces) by Johannes Rudolph
2:30 - 2:40 p.m.Presentations on work at Duke (Elevation, Mulitple Alignment, Persistence, Algebra) by Pankaj Agarwal and Herbert Edelsbrunner
2:40 - 2:50 p.m.Presentation on work at Stanford (Geometry to Combinatorics, Spanners, Energy Function, Loops, Characterize Motion) by Leo Guibas and Jean-Claude Latombe
2:50 - 3:15 p.m.Presentation on work at UNC Chapel Hlll (Almost Delaunay, Dynamic Programming, Inverse Kinematics, Structure Function Relationship, Family-specific Motifs, Statistical Potential) by Jack Snoeyink and Alex Tropsha
3:15 - 3:30 p.m.Presentation on work at NCA&T (Computational Quantum Chemistry, Schrödinger Equation, Prediction of Molecular Crystal Structures) by Robert Gdanitz
Student Presentations 3:30 - 3:50Persistence Diagrams as Stable Signatures of Proteins?by Dmitriy Morozov (Duke)
3:50 - 4:15Proton Packing to Assess the Quality Measure of NMR Structuresby Andrew Ban (Duke)
4:15 - 4:35Motifs in Protein-Protein Interfacesby Jeff Phillips (Duke)
4:35 - 5:00 p.m.Break
5:00 - 5:20Real Space Protein Model Completion: an Inverse Kinematics Approachby Itay Lotan (Stanford) view presentation (ppt)
5:20 - 5:40Structure-based Function Inference Using Family-Specific Subgraph Fingerprints Mined from Protein Familiesby Deepak Bandyopadhyay (UNC)view presentation (ppt)
5:40 - 6:00A Non-pairwise Decomposable Energy Function to Describe Hydrophilic Desolvation by Andrew Leaver-Fay (UNC)
6:00 - 6:20Forward and Inverse Kinematics in RNA Backbone Conformationsby Xueyi Wang (UNC) view presentation (ppt)
Business Meeting 6:30 - 7:30 p.m.Business Meeting for PIs
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