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| Connectivity | |
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Topological persistence (Edelsbrunner; Letscher, Zomorodian) |
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Writhing number of knots (Edelsbrunner; Agarwal, Wang) |
| Design and Stability | |
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Four-body potentials for proteins (Carter; Kettner, Snoeyink, Tropsha, Zhang) |
| Probabilistic Roadmaps | |
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Capturing molecular energy landscapes with probabilistic conformational roadmaps (Latombe; Apaydin, Brutlag, Singh) |
| Similarity and Structure | |
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Binding specificity of PXR (Snoeyink; Berretty, Mascarenhas, Redinbo) |
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Shape-basis for protein structures (Guibas; Koehl, Kolodny, Levitt) |
| Simulation | |
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Data structures for moving objects (Agarwal: Har-Peled) |
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Derivatives for molecular skin (Edelsbrunner; Cheng) |
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Implicit solvent representation / Area derivatives (Edelsbrunner; Bryant, Koehl, Levitt) |
| Software and Visualization | |
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Alpha shapes as a molecular geometry library (Edelsbrunner; Ban, Kettner, Snoeyink) |
| Structure Determination | |
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Contour trees for electron density data (Snoeyink; Carr, Kettner, Mascarenhas) |
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Morse complexes (Edelsbrunner: Harer, Zomorodian) |
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Sayre-type convolutional equations and crystallograpic phase refinement (Carter; Roach) |
| Surface Representation | |
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Protein surface mesh collection (Edelsbrunner, Rudolph, Natarajan) |
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Surface meshing (Edelsbrunner; Cheng, Dey, Sullivan) |
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Surface representations (Snoeyink; Isesnburg) |