Research Spaces
Work Station
Work Station is Wawe's precision molecular docking and simulation workspace. It orchestrates protein–ligand docking, molecular dynamics (MD) simulations, free energy perturbation (FEP) calculations, and multi-step pipeline automation — all accessible through a conversational interface and structured file upload panels.
Running a Docking Job
Docking jobs require a receptor file (PDB) and a ligand file (SDF or SMILES). Both can be uploaded directly in the Work Station interface or specified by PDB ID.
Upload or specify your receptor
Use the file upload panel on the left sidebar to upload a .pdb file, or type a PDB ID (e.g. 6LU7) and Wawe will fetch it from RCSB automatically. Ensure the structure is prepared (hydrogens added, waters removed) for best results — Wawe can do this for you on request.
Provide your ligand
Upload an .sdf file or paste a SMILES string directly in the chat. You can dock multiple ligands in one run by uploading a multi-conformer SDF.
Define the binding site
Specify residues that define the active site (e.g. "use the ATP binding pocket around His41 and Cys145") or provide a grid box centre and dimensions. Wawe will confirm the site before running.
Submit and monitor
Results appear inline once the job completes. You receive a binding pose visualisation, docking score (kcal/mol), key contact residues, and a downloadable pose file.
Docking jobs run on Wawe's compute grid. Typical wall time is 2–8 minutes depending on ligand count and box size. You will receive an email notification when the job completes.
Molecular Dynamics (MD) Simulations
After docking, you can launch an MD simulation to assess binding stability over time. Wawe uses GROMACS under the hood and handles force field assignment, solvation, energy minimisation, and equilibration automatically.
- Force fields supported — AMBER99SB-ILDN, CHARMM36, GROMOS96
- Simulation length — 10 ns default; custom lengths up to 1 µs available
- Analysis outputs — RMSD, RMSF, radius of gyration, contact maps, binding free energy estimate
Free Energy Perturbation (FEP)
FEP calculations provide high-accuracy relative binding free energy (RBFE) estimates between pairs of compounds, invaluable for lead optimisation. Configure an FEP run by specifying the reference compound and the perturbation series in the chat.
Pipeline Orchestration
Chain multiple docking, MD, and analysis steps into automated pipelines. Describe your workflow in plain language and Wawe will configure the pipeline graph:
- ›"Dock all 50 compounds, filter by score < −8 kcal/mol, run MD on top 5, rank by RMSD stability"
- ›"Perform blind docking on PDB 6LU7, cluster poses, extract top cluster centroid, calculate FEP vs reference"