Computational
biology and bioinformatics on the Duke Campus
by John Harer (Duke)
Impact and outreach in the
Biogeometry project
by Herbert Edelsbrunner (Duke)
Outreach programs for undergraduates at Duke
by Martha Absher (Duke)
Project overview: past, present,
and future
by Herbert Edelsbrunner (Duke)
10:00
Break
10:30
Macromolecular structures: a
user's perspective
by Michael Word (GlaxoSmithKline)
11:00
COMPUTATIONAL METHODS
Leader: Leo Guibas
Computing the Delaunay triangulation for PDB data
by Leo Liu (UNC)
Medial-axis based methods for automated ligand structure
extraction from density maps
by Daniel Russel (Stanford)
Critical point and flow structure for density data
by Vijay Natarajan (Duke)
Mesh refinement for Jacobi curves
by Alper Üngör (Duke)
12:30
Lunch
2:00
DOCKING AND BINDING
Leader: Johannes Rudolph
Covering rotations in 3D using quaternions by Abhijit Guria (Duke)
Points of maximal elevation on a
molecular surface by Yusu Wang (Duke)
Local search in docking configuration space
by Vicky Choi (Duke)
Information within the interface surace of a protein
complex
by Andrew Ban (Duke)
3:30
Break
4:00
SIMILARITY AND CLASSIFICIATION
Leader: Pankaj Agarwal
Input sensitive algorithms for multiple sequence alignment
by Rachel Kolodny (Stanford)
Four-body statistical scoring functions for protein
fold recognition
by Bala Krishnamoorthy (UNC)
Accurate classification of protein structural families
using coherent subgraph analysis
by Luke Huan (UNC) and Ruchir Shah (UNC)
Projective k-means clustering
by Nabil Mustafa (Duke)
7:00
Buffet dinner at Sitar India Palace
8:30
Coffee and rolls
9:00
MAINCHAIN
AND SIDECHAINS
Leader: Jack Snoeyink
Probik: manipulating protein backbones with inverse
kinematics
by David O'Brien (UNC)
Backbone motion in protein design
by Andrew Leaver-Fay (UNC)
Combinatorial rigidity for analyzing protein flexibility
by Andrea Mantler (UNC)
Automatic solution of missing links for automatically
resolved protein crystal structures
by Itay Lotan (Stanford)
10:30
Break
11:00
POTENTIALS AND ENERGY
Leader: Patrice Koehl
Progress on stochastic roadmap
simulation: non-uniform sampling
by Serkan Apaydin (Stanford)
The second derivative of the weighted volume of
a space-filling diagram
by David Cohen-Steiner (Duke)
Development of novel geometrical chemical descriptors
and their application to the prediction of ligand-receptor binding
affinity
by Shuxing Zhang (UNC)
Very large-scale computations of the free energies
of eight low-lying structures of arginine in the gas phase
by Robert Gdanitz (NCAT)
1:00
CLOSING REMARKS by John Staudhammer (NSF)
1:30
Lunch
Location: LSRC Building, Room D344 for all sessions
