From target to ranked
peptide candidates.
Raptorbind orchestrates the full peptide binder discovery workflow — structure preparation, RFdiffusion generation, docking, molecular dynamics, ADMET and toxicity prediction — in one reproducible run.
The 9-phase discovery pipeline
Every run executes the same reproducible chain — from target fetch to molecular dynamics and toxicity prediction.
Structure Preparation
Fetch the target structure from RCSB.
PDBFixer
Clean and repair the PDB structure with PDBFixer (missing residues/atoms, nonstandard residues, etc.).
RFdiffusion (Binder Generation)
Generate candidate peptide binders with RFdiffusion using the fixed PDB.
PDB → SDF Converter
Integrated PDB→SDF converter: converts the rank-1 RFdiffusion binder PDB into an SDF ligand.
DiffDock (Docking)
Dock the SDF ligand back into the fixed receptor with DiffDock-L.
RIGOR (Post-docking Triage)
Novel in-house deterministic post-docking triage (CIRS, HARP, ECHO, BALM → FUSE). Filters structurally fragile or chemically unrealistic poses before molecular dynamics.
Ligand Prep (SDF → PDB)
Convert the rank-1 DiffDock pose (SDF) into a PDB file ready for GROMACS molecular dynamics.
GROMACS (Molecular Dynamics)
Run a GROMACS molecular-dynamics simulation on the fixed receptor (Phase B) with the rank-1 DiffDock ligand (Phase G).
ADMET-AI
Predict ADMET properties of the rank-1 chain-B ligand SDF (Phase D output) with ADMET-AI. Runs in parallel with docking — does not block the main chain.
eTox Drug Toxicity
Predict drug toxicity of the rank-1 chain-B ligand SDF (Phase D output) with eTox Drug Toxicity Prediction. Runs in parallel with docking — does not block the main chain.
Meet RIGOR-Lite — our post-docking triage
An explainable scoring phase inserted between DiffDock and GROMACS that ranks docked peptide poses with CIRS, HARP, ECHO, BALM and FUSE — so expensive MD only runs on candidates worth simulating.
Built for serious in-silico work
Real outputs, your own keys, full traceability — no hidden steps.
Full orchestration
One submission triggers all 9 phases — auto-chaining, side-branches and resubmission included.
Real model outputs
Verbatim PDBs, SDFs, docking poses, MD trajectories, ADMET and eTox tables — downloadable.
Your data, your keys
Your API key stays in your settings. RLS keeps every project scoped to your account.
Smart resubmits
Re-run any phase from D onward with regenerated chain-B SDF — no need to restart from scratch.
Per-phase reports
Each phase gets its own panel: binder, docking, ligand prep, MD, ADMET, eTox.
Side-branch parallelism
ADMET and eTox fire in parallel with docking — failures never block the main chain.
How a Raptorbind run works
Three steps, one ranked report.
Pick a target
Drop in a PDB ID or upload a structure, choose chain and binding site, set peptide length and candidate count.
Tune & launch
Optionally adjust RFdiffusion, DiffDock and GROMACS parameters in advanced mode — or accept the defaults.
Read the report
Watch each phase complete in real time, then open the report for binders, poses, MD, ADMET and toxicity.
- Auto-fetches structures from RCSB
- PDBFixer cleans before generation
- Rank-N fallback if rank-1 fails
- Resubmit any phase independently
- Side-branch ADMET + eTox
- Downloadable per-file outputs
Ready to design your first binder?
Create an account, plug in your API key, and launch a full pipeline in minutes.