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Structural > Docking & Homology

3D-Dock Suite
FTDock, RPScore and MultiDock
Amber is the collective name for a suite of programs that allow users to carry out molecular dynamics simulations, particularly on biomolecules.
AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.
First fully automated Protein-Protein Docking web server.
Insight II
Insight II provides a comprehensive, integrated molecular graphics environment for visualization, protein engineering, macromolecular simulations, homology modeling, and de novo ligand design, enabling researchers to gain early insights into the structure and function of their targets of interest.
Using a sequence alignment, MODELLER generates a homology model.
SYBYL is a suite of computational informatics software designed to enhance the drug discovery workflows and decision-making of today's computational chemists and molecular modelers.
SWISS-MODEL is a fully automated protein structure homology-modeling server, accessible via the ExPASy web server, or from the program DeepView (Swiss Pdb-Viewer).
ZDOCK includes two protein docking algorithms, designed to operate in succession: a rigid-body docking program and a refinement program.
The eHiTS (electronic High Throughput Screening) software provides flexible ligand docking at speed approaching the crude virtual high throughput screening methods.