SAMSON Extensions Tutorials#
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#
- 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
- 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#
DNA origami#
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
- Universal Force Field