BIOLOGY
Protein Design
Protein backbone motion
(Hellinga, Snoeyink; Looger, Noonan, Jane and Dave Richardson)
Combinatorial rigidity and protein flexibility
(Snoeyink; Kolodny, Kuhn, Mantler, Streinu, Whiteley)
Structure Determination
Structure determination from nuclear Overhauser effect
(Bililign; Gdanitz)
Phase refinement using multi-atom fragments
(Carter; Roach, Scott)
Hydrogen placement in PDB
(Snoeyink; Leaver-Fay, Liu, Word)
Electron structure computations on molecules of biological interest
(Bililign; Gdanitz, Taddele, Wedderburn)
Structure Prediction
Protein-protein docking
(Agarwal, Edelsbrunner, Rudolph; Bespamyatnikh, Choi, Guria, Wang)
Prediction of molecular crystal structures
(Gdanitz; Snoeyink)
Implicit solvent modeling: volumes and areas of proteins
(Edelsbrunner, Koehl, Levitt; Bryant)
Monte Carlo simulation of HP-linkage folding
(Guibas, Levitt; Kolodny)
Alpha complex potentials for proteins
(Guibas, Koehl; Zomorodian)
Monte Carlo chain folding with Delaunay statistical potentials
(Carter, Snoeyink; Kettner, Leaver-Fay, O'Brien, Tropsha)
Protein-potentials from surface and buried triangles
(Snoeyink; Leaver-Fay, Tropsha)
MODELING
Shape Representation
Characterization of protein interfaces
(Edelsbrunner, Rudolph; Ban)
Combinatorial Morse theory
(Edelsbrunner, Guibas; Bremer, Hamann, Harer, Natarajan, Pascucci, Zomorodian)
Reeb graphs and Jacobi sets
(Edelsbrunner, Snoeyink; Cole-McLaughlin, Mascarenhas, Natarajan, Pascucci, Ungor)
Shape Descriptors/Features
Almost-Delaunay tetrahedra
(Snoeyink; Bandyopadhyay, Tropsha)
ALGORITHMS
Deformation
Maintenance of protein representations using spanners and independent complexes
(Agarwal, Edelsbrunner, Guibas; Gao, Nguyen, Russel, Wang, Yu)
Efficient updating of Delaunay triangulations in physical simulations
(Guibas; Russel)
Determining motion from protein conformations
(Carter, Snoeyink; Hsu)
Conformational Spaces
Stochastic roadmap simulation
(Latombe; Apaydin, Brutlag, Hsu, Lotan, Singh)
Shape Organization/Matching
Similarity measures for protein structures
(Agarwal, Guibas, Latombe; Har-Peled, Kolodny, Linial, Lotan, Mustafa, Wang)
Multiple sequence alignments
(Agarwal; Kolodny)
High dimensional clustering
(Agarwal)
Simulation
Simulation of cells in germinal center
(Latombe; Wong)
Fast Monte Carlo simulation
(Latombe; Lotan, Schwarzer, Moroz)
Visualization
Compression for surface models
(Snoeyink; Isenburg)