Protein Structure Prediction  |  ProteinShop  |  DockingShop  |  POSE Local Minimizations

Protein Structure Prediction We have developed a new method to predict the tertiary structure of "new fold" proteins. This method is one of the few attempts to use an all-atom physics-based energy function throughout all stages of the minimization. It uses some knowledge from known proteins to guide the search through the vast conformational spaceMore...

ProteinShop is an interactive tool for manipulating protein structures. It was designed to quickly create a diverse set of initial configurations for a given sequence of amino acids.

DockingShop is an integrated environment that permits interactive molecular docking by navigating a ligand or protein to an estimated binding site of a receptor with real-time graphical feedback of scoring factors as visual guides.

POSE is a graphical, interactive environment for the design, modeling, and optimization of protein structures. POSE will support interactive, user-driven monitoring and steering of a protein structure prediction process but the resulting infrastructure will easily translate to protein-protein interactions and RNA modeling.

Local Minimizations

Approaches for Local Minimizations

  We are working on efficient methods for large-scale local minimizations. Current approaches take many hours to converge. We propose to develop fast, sequential and parallel, local optimization methods that are applicable to large-scale problems.