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 |
| 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) |