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Structural > Docking & Homology > Modeling

Amber
Amber is the collective name for a suite of programs that allow users to carry out molecular dynamics simulations, particularly on biomolecules.
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.
Modeller
Using a sequence alignment, MODELLER generates a homology model.
SYBYL
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
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).