Summary

The second meeting of the ITR Bio-Geometry Project took place at Stanford University on October 22-23, 2001. The presentations were, throughout, of a technical nature and many, if not most, can be traced back to general discussions in the first meeting. Most talks were given by post-docs and students working with PIs on various problems in bio-geometry. We see from the program that a range of problems on the circular spectrum
Biology-Modeling-Algorithms-Software
which form the icon of the Bio-Geometry Project have been studied.

An ordering principle that emerged during the last half day of the meeting characterizes projects as biological or geometric, and within these categories as problems or methods. The resulting four categories are viewed in a linear sequence, with the justification that biological methods serve biological problems. The same can be said for geometry, and within this project, geometric problems are derived from biological methods. We will see in the future whether this linear metaphor serves as a useful ordering mechanism for work in bio-geometry.

bio-problems bio-methods geo-problems geo-methods


folding

docking

protein-protein
interaction

fitting

design

 


x-ray
crystallography

force fields

molecular dynamics/
hierarchical

NRM/motion
acquisition

shape libraries

stability measures/
disassociation
rates

decoy generation

implicit solvent
collision detection

complementarity/
similarity

density functions

motion
representations/
motion clusters

shape analysis

shape indexing

electrostatic
comput.


roadmaps

combinatorial
optimization

Morse complexes/
contour trees

bounding volume
hierarchies

alpha shapes

writing numbers

clustering

multi-resolution

software