SAMSON Extensions Tutorials

Use this page to choose the right SAMSON extension tutorial for your task. Most tutorials are hands-on and are best followed with SAMSON open so you can perform each step as you read.

Before you start:

• add the extension mentioned in the tutorial
• load the sample system or input data when the page asks for it
• use the category below that best matches your scientific goal

Below are the main tutorial paths available in this Documentation Center.

Drug discovery and structural biology

• Compute 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
• Create coarse-grained models for the MARTINI force field using Martinize2
• Dock ligands and ligand libraries with AutoDock Vina Extended
• Generate a transition path between protein structures with ARAP Interpolation
• Generate symmetry mates for proteins
• Interactive Ramachandran Plot
• Ligand Path Finder
• Molecular Restrainer: Energy Minimization for NMR-Derived Structures
• Strain Explorer: analyze ligand strain and compare relaxed conformations
• Perform Positional Analogue Scanning using the SMILES Manager
• Predict Biomolecular Structures
• Predict protein-ligand complexes using NMR2
• Prepare, minimize, equilibrate and simulate using GROMACS Wizard
• Protein alignment
• Protein docking with Hex
• Protein Path Finder
• Protein preparation & validation
• Run simulations in the cloud
• Symmetry detection in biological assemblies
• Using the RDKit - SMILES Manager

Materials science

• Build carbon nanotube models
• Generate crystal models

DNA origami

• Adenita SAMSON edition: Interactive 3D modeling and visualization of DNA nanostructures

Multi-domain extensions

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