Azulene Studio Docs
Run molecular simulation and prediction tools from the web app, the Python SDK, or the command line.
Get started
Section titled “Get started” Run your first job Install the CLI, log in, and submit a curated example.
Use the CLI or SDK Submit and track jobs from the command line with azulene jobs submit, or from Python with jobs.submit.
Binding Free Energy
Section titled “Binding Free Energy”How strongly molecules bind, on an absolute scale or relative to each other.
Absolute Binding Free Energy (ABFE) How strongly a single ligand binds a protein, on an absolute scale.
Relative Binding Free Energy (RBFE) Which of two similar ligands binds a protein more tightly, and by how much.
Relative Hydration Free Energy The free energy difference between two related molecules in solution.
Relative Hydration Free Energy for ncAAs Relative free energy for natural and unnatural amino acid changes.
Free Energy Methods
Section titled “Free Energy Methods” Protein Mutation Folding Stability (Physics-based ΔΔG) How a mutation changes a protein's folding stability.
Molecular Properties
Section titled “Molecular Properties”Solvation, reaction, permeation, solubility, and ADMET properties from a structure.
Absolute Hydration Free Energy The free energy of moving a molecule into water.
Absolute Solvation Free Energy (Non-Aqueous) The free energy of moving a molecule into a non water solvent.
Solvent Transfer Free Energy The free energy of moving a molecule between two solvents.
Aqueous Reaction Free Energy The free energy change of a reaction in water.
Deprotonation Free Energy (pKa) The free energy of removing a proton from a molecule.
Lipid Bilayer Permeation Free Energy How easily a molecule crosses a lipid membrane.
Aqueous Solubility (logS) Prediction A predicted water solubility value from a SMILES string.
ADMET Profile Prediction A multi endpoint ADMET profile with triage scoring.
Structure Prediction
Section titled “Structure Prediction”Predict 3D structures of proteins and complexes from sequence.
Boltz-2 Structure + Affinity Prediction Predicts a 3D structure and a binding affinity.
Chai-1 Complex Structure Prediction Predicts a 3D biomolecular structure.
OpenFold3 Complex Structure Prediction Predicts a 3D structure with the OpenFold3 model.
OpenFold2 Protein Structure Prediction Predicts a 3D structure with the OpenFold2 model.
ESMFold Single-Chain Structure Prediction Fast single chain structure prediction from a sequence.
Structure Based Drug Design
Section titled “Structure Based Drug Design”Place and score ligands in a protein pocket.
Docking Places a ligand in a protein pocket and scores the pose.
Covalent Docking Docks a ligand that forms a covalent bond to the protein.
Cofactor & Ligand Docking Docks molecules into the same site in order, keeping each placed molecule for the next stage.
Protein-Ligand Pose Refinement Optimizes docked poses with a machine learning model.
Protein-Ligand Scoring Scores docked poses with a machine learning model.
Structure Generation
Section titled “Structure Generation”Build 3D structures of small molecules and peptides.
3D Molecular Conformer Generation Generates 3D conformers for a molecule.
Peptide 3D Structure Generation (HELM) Builds a 3D peptide structure from a HELM string.
Protein Sequence Models
Section titled “Protein Sequence Models”Embeddings and mutation scores from protein language models.
ESM-2 Protein Sequence Embeddings Numeric embeddings for a protein sequence.
ESM-2 Zero-Shot Mutation Scoring Scores mutations without any training labels.