Dock libraries of ligands into proteins and rank them with AutoDock Vina.

Compute low-energy conformers of small molecules.

Build a graphene model from a TEM image

Prepare, minimize, equilibrate, and simulate systems using GROMACS.

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

[Deprecated since SAMSON 0.8.0] Create animation from a list of conformations

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

A demo of Adaptively Restrained Particle Simulations (ARPS), an adaptive simulation technique able to focus computations on the most mobile degrees of...

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

Perform protein-ligand docking thanks to AutoDock Vina.

Dock libraries of ligands into proteins and rank them with AutoDock Vina.

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.

This element has been made in order to help students discover the Lennard Jones interactions. It is a game in which the goal is to optimize the atoms'...

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.

Equidistant Uniform Rigid-body Ensemble CONstructor. Here we presented a fast algorithm for the construction of rigid-body conformational ensembles, ...

Export atoms along paths in PDB files.

Optimize molecular structures with FIRE.

Basic visual model to show cartesian axis. Open a new visual model and select "Frame axis" to see the frame axis as arrows, lines or both.

Build a graphene model from a TEM image

Create a graphene sheet in one click.

Generate structural models for simulations (add hydrogens, etc) using the GROMACS setup App. Simulate molecular systems using GROMACS force fields.

Prepare, minimize, equilibrate, and simulate systems using GROMACS.

Prepare and minimize systems using GROMACS. A free version of GROMACS Wizard.

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

Find and visualize hydrogen bonds: O−H···:N, O−H···:O, N−H···:N, N−H···:O, F−H···:F.

Simulate molecular systems using the IM-UFF (Interactive Modeling - Universal Force Field) with automatic forming and breaking of bonds.

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

This editor rotate the molecule by defining rotation axis and rotation angle. The user define the rotation axis (represented by an arrow in the view) ...

This SAMSON Element contains a Lennard-Jones interaction model that may be used for several purposes: teaching, learning about van der Waals interacti...

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 output? This Element redirects C/C++ standard streams and Qt messages.

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

Create a carbon nanotube in just two clicks.

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...

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

Convert between a path and a series of conformations. - For path -> conformations. Select a path or several paths from Document View in SAMSON, open ...

The app can save a path or several paths to a pdb or separate pdb file(s). It can even save a list of conformations to a pdb or separate pdb file(s)....

Visualize paths of a set of atoms.

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

Rapidly compute small-angle X-ray scattering profiles.

Visualize MOFs and crystals with Polyhedrons

Align multiple sequence (based on the MUSCLE software) and structures.

Fetch molecular structures from the RCSB Protein Data Bank (PDB).

Find protein conformational transition paths within minutes.

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

Script everything. Access the SAMSON API through Python. Model and simulate from scripts. Pipeline calculations. Integrate other Python packages.

This app calculates RMSD between 2 structures. If it is an amino acid chains, a sequence alignment of the structures is needed (in fasta format). The ...

Tutorial for SAMSON : Basic functionnalities. Learn how to create, move and delete an atom, and then create a basic molecule thanks to a step-by-step ...

Want to create a SAMSON Element? Easily generate an empty SAMSON Element from a template and start developing.

Package and validate a SAMSON Element you developed for further publishing on samson-connect.net.

Generate UUID directly from SAMSON in one click.

Basic geometry and concentration statistics for the selected atoms.

Module for the interactive exploration of chemical reactivity. This element implements ultra-fast quantum-chemical methods that are orders of magni...

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...

Import Stereolithography (.stl) binary and ASCII files. Visualize them. Generate carbon atoms based on stl files to create quickly new original atomic...

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.

[Deprecated since SAMSON 0.7.0] This app imports selected pdb files as a trajectory (a set of conformations).