SAMSON Connect | Extensions

SAMSON Extensions

Free forever for academic & nonprofit non-commercial use.
SAMSON and all SAMSON Extensions are free for non-commercial use.
This includes extensions for docking, simulating, animating, scripting, etc.

Most features run locally for free. Some optional calculations run in the cloud,
such as structure prediction and cloud simulations, and require computing credits.


Commercial plans start with a free 30-day trial of the Expert plan.
No credit card required to start. Subscribe anytime. Cancel anytime.
Any question? Send us an email or schedule a short call.
Featured
ANDROMEDA Demo
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
1347
75
1

Predict molecular ADME/PK properties in humans with this demo of ANDROMEDA by Prosilico.

Biomolecular Structure Prediction

Included with all plans

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

Interaction Designer

Included with all plans

Visualize and design molecules and interactions.

Molecular Cycles

Included with all plans

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

Protein Aligner

Included with all plans

Align multiple sequences and structures of proteins.

SAMSON AI ✨

Included with all plans

Your next-generation modeling assistant.

Life science
ANDROMEDA Demo
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
1347
75
1

Predict molecular ADME/PK properties in humans with this demo of ANDROMEDA by Prosilico.

ARAP Interpolator
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
3290
262
3

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

AutoDock Vina Extended

Free trial

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

Batch Protein Prepare
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
2453
142
1

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

Biomolecular Structure Prediction

Included with all plans

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

Conformer Creator

Free trial

Compute low-energy conformers of small molecules.

FITTED Suite

Free trial

28357
57
3

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

Glycans
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
2808
66
3

Build glycans using a library of monosaccharides

GROMACS Wizard

Free trial

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

Hex

Free trial

Perform protein-protein docking.

Hydrogen Bond Finder
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
4170
967
5

Find and visualize hydrogen bonds.

IM-UFF

Free trial

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

Interaction Designer

Included with all plans

Visualize and design molecules and interactions.

Interactive Ramachandran Plot
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
3908
822
3

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

iSafeRat MechoA
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
3654
408
3

Predict mechanisms of toxic action of molecules.

Ligand Path Finder

Free trial

Find ligand unbinding pathways from a protein within minutes.

Martinize
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
2021
44
1

Create coarse-grained models for the MARTINI force field.

MMTF Importer

Included with all plans

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

Molecular Box Builder
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
3276
134
4

Construct systems by filling a box with molecules.

Molecular Restrainer
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
863
29

Apply restraints to a molecular system and minimize them.

NMR2

Free trial

2732
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1

Compute structures of protein-ligand complexes using NMR data.

Normal Modes Advanced

Free trial

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

Normal Modes Analysis
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
3276
507
1

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

OpenMM Wizard

Free trial

Setup and run simulations with OpenMM.

PDBFixer
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
6123
102
1

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

PDBx/mmCIF Importer

Included with all plans

Importer for the PDBx/mmCIF file format.

Protein Aligner

Included with all plans

Align multiple sequences and structures of proteins.

Protein Path Finder

Free trial

Find protein conformational transition paths within minutes.

Protein-Ligand Interaction Analyzer
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
4883
460
5

Analyze protein-ligand interactions

Rotamers editor
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
3311
178
5

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

SAMSON AI ✨

Included with all plans

Your next-generation modeling assistant.

SMILES Manager

Free trial

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

Structure validation

Included with all plans

Validate biological structures and prepare them for further calculations.

Structures Fetcher

Included with all plans

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

Symmetry Detection
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
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3

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

Symmetry Mate Editor
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
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2

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

Machine learning and AI
ANDROMEDA Demo
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
1347
75
1

Predict molecular ADME/PK properties in humans with this demo of ANDROMEDA by Prosilico.

Biomolecular Structure Prediction

Included with all plans

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

SAMSON AI ✨

Included with all plans

Your next-generation modeling assistant.

Materials science
Bond Angle Distribution
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
2540
378
1

Compute the bond angle distribution of the selected atoms.

Bond Distortion Visualisation
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
2671
393
1

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

Brenner interaction model

Free trial

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

Conformer Creator

Free trial

Compute low-energy conformers of small molecules.

Crystal Creator

Free trial

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

Graphene Image Analyzer

Free trial

Build a graphene model from a TEM image

Graphene Sheet Creator
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
4519
1817
6

Create a graphene sheet in one click.

IM-UFF

Free trial

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

Molecular Box Builder
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
3276
134
4

Construct systems by filling a box with molecules.

Molecular Motif Grafter
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
2166
52
2

Place molecules on a surface

Nanotube Creator
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
6809
1740
5

Create a carbon nanotube in three clicks.

P-NEB
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
4135
236
1

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

Polymer Builder
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
3281
118
1

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

SAMSON AI ✨

Included with all plans

Your next-generation modeling assistant.

TMD Image Analyzer

Free trial

Construct transition metal dichalcogenide monolayers from experimental images.

Twister

Included with all plans

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

Computational chemistry
Adaptive Lennard-Jones
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
2752
488
1

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

Brenner interaction model

Free trial

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

Conformer Creator

Free trial

Compute low-energy conformers of small molecules.

FIRE state updater
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
3313
756
2

Optimize molecular structures with FIRE.

GROMACS Wizard

Free trial

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

iSafeRat MechoA
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
3654
408
3

Predict mechanisms of toxic action of molecules.

Lennard-Jones model
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
3002
1151
1

The Lennard-Jones interaction model.

OpenMM Wizard

Free trial

Setup and run simulations with OpenMM.

P-NEB
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
4135
236
1

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

SMILES Manager

Free trial

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

State Updaters Collection

Included with all plans

A collection of state updaters used for interactive minimization simulation.

Universal force field

Included with all plans

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

Physics and nanotechnology
Brenner interaction model

Free trial

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

Graphene Image Analyzer

Free trial

Build a graphene model from a TEM image

Graphene Sheet Creator
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
4519
1817
6

Create a graphene sheet in one click.

Molecular Box Builder
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
3276
134
4

Construct systems by filling a box with molecules.

Molecular Motif Grafter
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
2166
52
2

Place molecules on a surface

Nanotube Creator
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
6809
1740
5

Create a carbon nanotube in three clicks.

Pattern Builder

Included with all plans

Rapidly build advanced patterns.

TMD Image Analyzer

Free trial

Construct transition metal dichalcogenide monolayers from experimental images.

Teaching and learning
Cluster Game
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
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3

A game where you build optimal assemblies of interacting atoms.

Discovering Alkanes
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
3519
154
3

A game where you search and build molecules.

Documentation Links

Included with all plans

Preview and access the User guide pages directly from SAMSON.

Interactive Tutorials

Included with all plans

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

SAMSON AI ✨

Included with all plans

Your next-generation modeling assistant.

Virtual Reality Portal
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
3894
235
4

Visualize, build, and simulate in virtual reality.

Visualization and rendering
Animation Toolkit

Included with all plans

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

Bond Angle Distribution
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
2540
378
1

Compute the bond angle distribution of the selected atoms.

Bond Distortion Visualisation
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
2671
393
1

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

glTF Importer and Exporter

In Professional plans and above

Import and export 3D models in glTF format.

Glycans Visual Models

Included with all plans

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

Image Loader

Included with all plans

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

Molecular Cycles

Included with all plans

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

Movie Exporters

Included with all plans

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

Pathlines
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
3307
282
2

Visualize paths/trajectories of a set of atoms.

Polyhedral visual model

Included with all plans

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

STL Importer

Included with all plans

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

Virtual Reality Portal
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
3894
235
4

Visualize, build, and simulate in virtual reality.

Visual Models Collection

Included with all plans

Visualize molecular structures using a collection of visual models.

Visual Presets

Included with all plans

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

Molecular modeling and editing
Assets Collection

Included with all plans

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

Atoms Selector
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
2468
433
1

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

Commands Collection

Included with all plans

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

Crystal Creator

Free trial

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

Editors Collection

Included with all plans

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

FIRE state updater
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
3313
756
2

Optimize molecular structures with FIRE.

Graphene Sheet Creator
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
4519
1817
6

Create a graphene sheet in one click.

IM-UFF

Free trial

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

Martinize
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
2021
44
1

Create coarse-grained models for the MARTINI force field.

Molecular Box Builder
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
3276
134
4

Construct systems by filling a box with molecules.

Molecular Motif Grafter
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
2166
52
2

Place molecules on a surface

Molecular Restrainer
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
863
29

Apply restraints to a molecular system and minimize them.

Nanotube Creator
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
6809
1740
5

Create a carbon nanotube in three clicks.

Pattern Builder

Included with all plans

Rapidly build advanced patterns.

PDBFixer
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
6123
102
1

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

Polymer Builder
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
3281
118
1

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

Rotamers editor
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
3311
178
5

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

SAMSON AI ✨

Included with all plans

Your next-generation modeling assistant.

Selection statistics
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
2387
266
1

Basic geometry and concentration statistics for the selected atoms.

Selectors Collection

Included with all plans

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

Structure validation

Included with all plans

Validate biological structures and prepare them for further calculations.

Twister

Included with all plans

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

Workspaces Collection

Included with all plans

A collection of workspaces that customize the SAMSON interface.

Scripting and development
Code Editor

Included with all plans

Develop using the Monaco Editor.

Exposed functionality viewer
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
2116
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2

View the exposed functionality of SAMSON Extensions

Log Viewer
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
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3

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

Python Scripting

Included with all plans

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

SAMSON AI ✨

Included with all plans

Your next-generation modeling assistant.

SAMSON Extension Generator
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
3958
308
4

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

SAMSON Extension Packager
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
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3

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

Simple Script
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
3132
299
1

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

UUID Generator
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
3557
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1

Generate UUIDs directly from SAMSON in one click.

Data conversion and exchange
Export along paths
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
2757
279
1

Export atoms along paths in PDB files.

Exporters Collection

Included with all plans

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

glTF Importer and Exporter

In Professional plans and above

Import and export 3D models in glTF format.

Gzip Importer

Included with all plans

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

Image Loader

Included with all plans

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

Importers Collection

Included with all plans

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

Martinize
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
2021
44
1

Create coarse-grained models for the MARTINI force field.

MMTF Importer

Included with all plans

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

Movie Exporters

Included with all plans

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

OBJ Exporter

In Professional plans and above

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

OBJ Importer

Included with all plans

Import OBJ files into SAMSON.

PDB trajectory loader
This extension is free.

A Professional plan or above is required to
use more than one free extension at a time.
2971
345
1

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

PDBx/mmCIF Importer

Included with all plans

Importer for the PDBx/mmCIF file format.

STL Importer

Included with all plans

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

Trajectory Importers

Included with all plans

Import and export molecular dynamics trajectories in various formats.

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