Recent Projects

MAPS: Protein Docking Interfaces
Modeling flexible protein loops(Latombe, Dhanik, Lotan, Marz, Kou)
Prediction of possible molecular crystal structures using Monte-Carlo simulated annealing(Gdanitz; Agarwal, Edelsbrunner, Snoeyink)

Year 4 Projects covering September 2003 - August 2004

Computational Methods

Comparison of continuous function (Edelsbrunner, Harer, Natarajan, Pascucci)
Geometric spanners for proximity maintenance and collision detection (Gao, Nguyen, Guibas)

Docking and Binding

Protein-protein docking (Edelsbrunner; Agarwal, Chien, Choi, Headd, Mian, Rudolph, Wang)
Protein-protein interface surfaces (Edelsbrunner, Rudolph; Ban, Chen)

Gene Clusters

Clusters of orthologous groups (COGs) (Snoeyink; Falls, Powell)

Mainchains and Sidechains

Manipulating protein backbones and side chains of proteins (Snoeyink, Hellinga; Looger, Tian, O’Brien, Noonan, Leaver-Fay)
Modeling loops in protein structure: a fragment-based approach (Koehl, Guibas, Levitt; Kolodny)
Secondary structure prediction from sequence (Carter, Tropsha, Roach; Krishnamoorthy)

Motion and Trajectories

Combinatorial descriptions of folding processes (Russel, Zomorodian, Guibas)
Combinatorial rigidity and protein flexibility (Mantler, Snoeyink, Streinu, Whitely, Kuhn)
Fast Monte Carlo simulation (Latombe; Lotan)
Protein folding simulations (Tropsha, Snoeyink; O’Brien)
Smoothing molecular trajectories (Milosavljevic, Guibas)
Stochastic roadmap simulation (Latombe; Apaydin, Ieong)

Potentials and Energy

Almost-Delaunay triangulations (Snoeyink; Bandyopadhyay, Huan, Wang, Carter)
Efficient updating of Delaunay triangulations in physical simulations (Russel, Guibas)
Electronic structure calculations using density functional theory (DFT) (Bililign, Gdanitz, Wedderburn, Taddele)
Independent complexes (Attali, Edelsbrunner)
Protein dynamics with implicit solvent: a normal mode approach (Koehl, Edelsbrunner; Cohen-Steiner)
Statistical potentials (Tropsha, Snoeyink, Zhang)

Similarity and Classification

Comparison of protein structure alignment methods (Kolodny, Koehl, Levitt)
High-dimensional clustering (Agarwal; Mustafa)
Identification of substructural motifs characteristic of protein structural families (Tropsha, Snoeyink; Prins, Wang)
Multiple protein structure alignment (Carter, Roach; Sharma, Armwood)
Multiple sequence alignment using geometric ideas (Kolodny, Agarwal, Bilu)
A sequence approach to protein structure alignment (Koehl; Kolodny; Poch)
Shape similarity (Agarwal; Edelsbrunner, Bailey, Phillips, Varadarajan)
Stability of persistence diagrams (Cohen-Steiner, Edelsbrunner, Harer)

Software and Visualizaton

Fast weighted Delaunay triangulation code (Snoeyink; Liu)
Reeb graphs of a time-varying function (Edelsbrunner, Harer, Mascarenhas, Pascucci)
Related other research (Brooks)
Simulation of cells in germinal center (Latombe; Wong)

Structure Determination

Local squaring functions (Carter)
Missing loop problem in protein structure determination (Latombe; Lotan)
Prediction of possible molecular crystal structures using Monte-Carlo simulated annealing (Bililign, Gdanitz)
Theoretical biochemistry research (Bililign, Gdanitz, Basti)