Complementarity and Similarity
Binding specificity of PXR.
(Snoeyink; Hsu, Leaver-Fay, Mascarenhas, Redinbo, Watkins)
Protein docking by shape matching.
(Edelsbrunner; Agarwal, Bespamyatnikh, Mustafa, Rudolph, Sharir, Wang)
The definition and construction of interfaces for macromolecular complexes.
(Edelsbrunner; Ban, Rudolph)
Protein backbone matching.
(Agarwal; Mustafa, Venkatasubramanian, Wang)
High dimensional clustering.
(Agarwal; Procopiuc, Varadarajan)

Energy Potential and Protein Design
Backbone and sequence design.
(Hellinga; Dwyer, Looger, Wisz)
Almost-Delaunay triangulation for analyzing protein structure
(Snoeyink; Bandyopadhyay, Tropsha)
Implicit solvent modeling.
(Edelsbrunner; Bryant, Koehl, Levitt)

Density Analysis
Structure extraction from crystallography density data.
(Guibas; Brunger, Russel)
Local squaring functions and generalized density modifications.
(Carter; Roach)
Geometric and topological simplification of continuous functions.
(Edelsbrunner; Bremer, Harer, Natarajan, Pascucci)
Manifolds of simultaneous critical points.
(Edelsbrunner; Cole-McLaughlin, Harer, Natarajan, Pascucci)
The structure and simplification of Reeb graphs.
(Edelsbrunner; Cole-McLaughlin, Harer, Natarajan, Pascucci)

Structure and Stability
Investigation of stability and structure of metal-rare gas clusters.
(Bililign; Vaval)
Alpha-complex potentials for proteins.
(Guibas; Koehl, Zomorodian)
Four-body potentials for proteins.
(Carter; Kettner, Leaver-Fay, O’Brien, Snoeyink, Tropsha)
Libraries of protein fragments for structural modeling.
(Levitt; Guibas, Kolodny, Koehl)
Polygonal shape representations.
(Agarwal; Ban, Bespamyatnikh, Edelsbrunner, Har-Peled, Klein, Knauer, Mustafa, Sharir, Wang)

Motion and Roadmaps
Collision detection during simulated protein motion.
(Guibas; Agarwal, Halperin, Latombe, Lotan, Nguyen, Russsel, Schwarzer, Zhang)
Kinetic maintenance of inclusion/exclusion formulas.
(Guibas; Edelsbrunner, Koehl, Russel)
Identifying key motions in TrpRS and other proteins.
(Carter; Hsu, Snoeyink)
Nearest-neighbor search among large sets of protein conformations.
(Latombe; Lotan, Schwarzer)
Computing ensemble properties of molecular pathways using probabilistic conformational roadmaps.
(Latombe; Apaydin, Brutlag, Guestrin, Hsu, Singh, Varma)
Hierarchical probabilistic road maps.
(Agarwal; Collins, Harer)

Software and Visualization
Visualization with the PIT.
(Brooks; Bandopadhyay, Berretty, Slaughter, Snoeyink)
Surface and mesh compression.
(Snoeyink; Isenburg)
The Alpha Shapes software library.
(Edelsbrunner; Ban, Brady, Cheng, Kettner, Koehl, Zomorodian)