Welcome to SAMSON Extensions Tutorials

SAMSON Extensions Guides

SAMSON is an integrated molecular design platform with an open architecture: you can customize your SAMSON by adding free or paid extensions from the Marketplace.

Below are tutorials detailing how to use some of the most popular extensions.

Drug discovery and structural biology

• Aligning proteins
• Computing axes of symmetry of biological assemblies
• Computing normal modes that open a binding site
• Coronavirus: computing the opening motion of the SARS-CoV-2 spike
• Covalent and non-covalent protein-ligand docking with the Fitted Suite by Molecular Forecaster
• Docking ligands and ligand libraries with AutoDock Vina Extended
• Generating a path between protein structures
• Generating symmetry mates
• Interactive Ramachandran Plot
• Ligand Path Finder
• Perform Positional Analogue Scanning using the SMILES Manager

• Predicting protein-ligand complexes using NMR2

• Prepare, minimize, equilibrate and simulate using GROMACS Wizard

• Protein docking with Hex
• Protein Path Finder
• Running simulations in the cloud
• Using the RDKit - SMILES Manager

Materials science

• Building carbon nanotube models
• Construct polymers with Polymer Builder
• Generating crystal models

DNA origami

• Adenita SAMSON Edition: Interactive 3D modeling and visualization of DNA Nanostructures

Multi-domain extensions

• Create molecular boxes with Molecular Box Builder
• Export atoms trajectories along paths
• Fast geometry optimization with the FIRE minimizer
• Interactive Modeling Universal Force Field (IM-UFF)
• Making nano-batarangs (and more)
• Optimize transition paths with P-NEB
• Pathlines: show a path of the center of mass of an atomic system
• Universal Force Field