Table of Contents for Molecular Modeling and Simulation Applications

CNS: Dynamics Simulation (Local Only)
Coot: Model Building, Completion, and Validation
DOCK: Most Favorable Ligand/Receptor Binding
Gaussian 3.0 :Molecular structure prediction
GROMACS : Dynamics for Molecular Modeling
ISIS/DRAW: Chemical Structure Drawing package
MAIN : Model Building and Refinement
MODELLER : Protein Homology and Comparative Modeling
Moloc: Interactive manipulation in three diensional space
NAMD : Dynamics for Molecular Modeling
NAMOT : Nucleic Acid Modeling Tool
O : Model Building and Refinement
REDUCE : Build Hydrogens on your Model
RNAView : Quickly generate display of RNA/DNA secondary structures with tertiary interactions
ROSETTA: Prediction and design of protein structures, folding, and interactions
TINKER: Molecular Modeling, Dynamics and Analysis
TurboFrodo : Model Building and Refinement
WHAT_IF : Model Building and Refinement
Xplor : Dynamics Simulation
Xtalview : Model Building and Refinement