Simulate with an adaptive version of the Lennard-Jones potential.

Rapidly create advanced molecular animations with these thirty-two animation templates.

Generate paths between two protein conformations within a few seconds thanks to ARAP interpolation.

A collection of various assets that can be used to build molecular systems.

Select atoms based on expressions with NSL-like variables, standard mathematical and logical operations.

Dock thousands of ligands into proteins and rank them with this extended version of AutoDock Vina.

Prepare proteins in a batch: remove alt. locations, water, ligands, ions, add hydrogens.

Predict biomolecular structures using AlphaFold 2, Boltz-2 and Chai-1.

Compute the bond angle distribution of the selected atoms.

Visualize the angle, bond, and projected bond distortions of a molecular or crystalic structure.

Perform interactive simulations of carbon nanotubes, graphene and hydrocarbon systems. Build complex geometries thanks to this reactive force field.

A game where you build optimal assemblies of interacting atoms.

Develop using the Monaco Editor.

A collection of commands that constitute menus and allow you to perform tasks.

Compute low-energy conformers of small molecules.

Generate crystal models in a few clicks. Describe unit cells, import CIF files, model defects and impurities. Cut crystals.

A game where you search and build molecules.

Preview and access the User guide pages directly from SAMSON.

A collection of editors to build, modify, move, measure, and label molecular systems.

Export atoms along paths in PDB files.

A collection of exporters for the GRO, MOL2, PDB, and XYZ formats.

View the exposed functionality of SAMSON Extensions

Optimize molecular structures with FIRE.

Perform covalent and non-covalent protein-ligand docking with the FITTED Suite by Molecular Forecaster

Import and export 3D models in glTF format.

Build glycans using a library of monosaccharides

Visualize glycans with the 3D Symbol Nomenclature for Glycans (SNFG) representation.

Build a graphene model from a TEM image

Create a graphene sheet in one click.

Perform interactive simulations with GROMACS force fields.

Prepare, minimize, equilibrate, and simulate systems using GROMACS on your computer or in the cloud.

Importer for gzipped (.gz) files of already supported formats (e.g., .pdb.gz).

Perform protein-protein docking.

Find and visualize hydrogen bonds.

Simulate molecular systems using this generalized, Interactive-Modeling version of the Universal Force Field capable of automatic bond creation and br...

Load images as visual models or meshes to include them in visualizations and presentations, or to help you construct structures.

A collection of importers for the CML, GRO, MOL, MOL2, PDB, SD, SDF, and XYZ formats

Visualize and design molecules and interactions.

Display Ramachandran diagram of selected residues. Move a residue on the plot and see the effect it has on the protein.

Learn molecular design with SAMSON thanks to these interactive, step-by-step tutorials.

Predict mechanisms of toxic action of molecules.

The Lennard-Jones interaction model.

Find ligand unbinding pathways from a protein within minutes.

Find ligand unbinding pathways within minutes with the new ART-RRT method.

Want to check logs and outputs? This extension redirects C/C++ standard streams and Qt messages.

Create coarse-grained models for the MARTINI force field.

Importer for the macromolecular transmission format (MMTF) files (*.mmtf).

Construct systems by filling a box with molecules.

Make studio-quality visuals and animations with Cycles, the Blender renderer.

Place molecules on a surface

Apply restraints to a molecular system and minimize them.

Export animations and presentations as movies in GIF, MP4, and WEBM formats.

Create a carbon nanotube in three clicks.

Compute structures of protein-ligand complexes using NMR data.

Compute nonlinear normal modes that open and close binding pockets of proteins.

Compute the nonlinear normal modes of a molecular system (protein, RNA, DNA) very quickly using the NOLB algorithm developed by Alexandre Hoffmann and...

Export molecular structures, visual models and surfaces to OBJ - including their colors - to import them in 3D animation software, or even PowerPoint™...

Import OBJ files into SAMSON.

Setup and run simulations with OpenMM.

Use a parallel implementation of the nudged elastic band (NEB) method to find saddle points and minimum-energy paths.

Visualize paths/trajectories of a set of atoms.

Rapidly build advanced patterns.

Create a trajectory (path) based on a series of PDB files.

Fix problems in PDB files in preparation for simulating them: remove alt.locations, add missing resides and atoms, add solvent and membrane, etc.

Importer for the PDBx/mmCIF file format.

Rapidly compute small-angle X-ray scattering profiles.

Visualize Metal-Organic Frameworks (MOFs) and crystals with polyhedrons

Construct polymers out of various building blocks (monomers and their sequences).

Align multiple sequences and structures of proteins.

Find protein conformational transition paths within minutes.

Find protein conformational transition paths within minutes with the newly developed ART-RRT method.

Analyze protein-ligand interactions

Script SAMSON using Python. Model and simulate from scripts. Pipeline calculations. Integrate Python packages for machine learning and more.

Modify an amino acid residue into its rotamer or mutate it into an amino acid residue of a different type.

Your next-generation modeling assistant.

Want to create a SAMSON Extension ? Generate source code from a template in a few clicks and start developing.

Package and validate a SAMSON Extension you developed to publish it on SAMSON Connect.

Basic geometry and concentration statistics for the selected atoms.

A collection of selectors used across various commands, visual presets, and extensions.

Modify atoms' parameters (position, selection, etc) using a simple scripting language, NSL-like variables, mathematical and logical operations.

Import thousands of SMILES codes. Filter them using custom patterns. Modify them and generate their corresponding 2D image. Add them to the SAMSON Doc...

A collection of state updaters used for interactive minimization simulation.

Import Stereolithography (.stl) binary and ASCII files to display them and generate carbon atoms based on vertices positions.

Validate biological structures and prepare them for further calculations.

Fetch structures from the RCSB Protein Data Bank, the AlphaFold Protein Structure Database, ESM Metagenomic Atlas, PubChem, etc. Convert IUPAC and SMI...

Detect axes of cyclic, dihedral, and cubic symmetries in protein complexes.

Interactively generate symmetry mates of a protein based on the crystallographic information from a PDB file.

Construct transition metal dichalcogenide monolayers from experimental images.

Import and export molecular dynamics trajectories in various formats.

Perform large-scale deformations of materials and biomolecules interactively with this powerful editor.

Simulate molecular systems using the Universal Force Field (UFF) with automatic structure perception.

Generate UUIDs directly from SAMSON in one click.

Visualize, build, and simulate in virtual reality.

Visualize molecular structures using a collection of visual models.

A collection of visual presets to rapidly create publication-quality images.

A collection of workspaces that customize the SAMSON interface.