Connectivity
Topological persistence (Edelsbrunner; Letscher, Zomorodian)
Writhing number of knots (Edelsbrunner; Agarwal, Wang)

Design and Stability
Four-body potentials for proteins (Carter; Kettner, Snoeyink, Tropsha, Zhang)

Probabilistic Roadmaps
Capturing molecular energy landscapes with probabilistic conformational roadmaps (Latombe; Apaydin, Brutlag, Singh)

Similarity and Structure
Binding specificity of PXR (Snoeyink; Berretty, Mascarenhas, Redinbo)
Shape-basis for protein structures (Guibas; Koehl, Kolodny, Levitt)

Simulation
Data structures for moving objects (Agarwal: Har-Peled)
Derivatives for molecular skin (Edelsbrunner; Cheng)
Implicit solvent representation / Area derivatives (Edelsbrunner; Bryant, Koehl, Levitt)

Software and Visualization
Alpha shapes as a molecular geometry library (Edelsbrunner; Ban, Kettner, Snoeyink)

Structure Determination
Contour trees for electron density data (Snoeyink; Carr, Kettner, Mascarenhas)
Morse complexes (Edelsbrunner: Harer, Zomorodian)
Sayre-type convolutional equations and crystallograpic phase refinement (Carter; Roach)

Surface Representation
Protein surface mesh collection (Edelsbrunner, Rudolph, Natarajan)
Surface meshing (Edelsbrunner; Cheng, Dey, Sullivan)
Surface representations (Snoeyink; Isesnburg)