Computer Aided Drug Discovery

PlayMolecule is a virtual environment for computable drug discovery where algorithms, data and computers are integrated to discover new knowledge.

PlayMolecule allows:

  • Protein and Small Molecule Preparation
  • Library Design and Generation
  • Virtual Screening
  • Binding Mode Validation (MD)
  • Data Storage
  • Algorithmic Automation

You can try PlayMolecule for free on your browser by visiting playmolecule.com, no need for registration.

Click here to know more about Play, the flexible selling mechanism that fuels Playmolecule.

Different Apps for Different Problems

Target Preparation and Inspection


(All related apps: SystemBuilder, MembraneBuilder, ProteinPrepare, AcePrep, Parameterize, PlexView, DeepSite)

In-silico assays by molecular simulations

Study the conformational landscape of proteins and ligands using in silico methods.

(All related apps: SimpleRun, CrypticScout, In-silico conformational analysis, In-silico binding assays)

Chemical space exploration

Generate novel small molecules using machine learning models. You can generate new molecules by providing: 


(All related apps: Generative, LiGANN, LigDream, PathwayMap)

Virtual screening and affinity predictions

Award-winning docking and binding affinity algorithms.

  • Dock small molecules into protein pockets using different protocols: template docking, pharmacophoric restraints or free docking.
  • Re-score your docked compounds using pharmacophore overlap or machine learning algorithms.
  • Train your own model with your in-house data to then rescore your library of compounds.


(All related apps: AceDock, KDeep, KDeepTrainer, DeltaDelta, Glimpse)


There are several ways to interact with PlayMolecule. Choose the one that better fits your needs:


A powerful 3D viewer to interact and visualize all Acellera applications. Available as a local installation or as a web-app (requires Playmolecule Web Services).

Command Line
Command line execution

Execute each application from the command line.

Python API

Restful interface for managing all application components and running them in parallel on your cluster. Access and execute all applications programmatically using a powerful Python API.

Third-party integrations

PlayMolecule apps can be integrated into Knime, Pipeline pilot, PyMol. Use PyMol as your interface to Acellera’s applications as plugins. Acellera can provide support into integrating our technology into your proprietary system.


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