Protein/Ligand
TraceDDE
Model-agnostic physics verification layer
Turn AI-generated poses into auditable, claim-specific decisions.
Input: AI-generated poses
Supported pose models/pipelines, with associated metadata
Protein/Ligand
Protein/Ligand
Protein/Ligand
Protein/Ligand
Protein/Ligand
Protein/Ligand
Protein/Ligand
Protein/Ligand
Protein/Ligand
Protein/Ligand
Protein/Ligand
TraceDDE Verification Tiers
TIER 0: Chemistry & Identity
- Validate chemistry and parameters
- Check protonation, tautomers, Stereochemistry, etc.
TIER 1: Stability & Reproducibility
- Explicit-solvent MD
- Pose stability and robustness
- Stability, convergence checks
TIER 2: Kinetic Endpoint
- Rare-event sampling, MSM, OPES
- Rate estimation, uncertainty quantification
TIER 3: Affinity Extension (Gated)
- Alchemical methods
- Relative/absolute affinity
- Gate checks
Verified candidates
Where it sits
Discovery teams already use generative and predictive models to propose and rank molecules. TraceDDE sits after that proposal and before the decision to spend on experiments. It uses compiled adaptive enhanced sampling molecular simulation, through the TRACE engine, to examine whether a proposed candidate is physically plausible.
TRACE Performance
Peak acceleration
Up to 44×44× Faster
TRACE versus OpenMM + PLUMED on one NVIDIA A100.
NVIDIA A100Large protein systems
Average force difference
Averaged4.8×10⁻⁷ eV/Å
TRACE versus OpenMM + PLUMED, averaged across the four systems
Four systemsNVIDIA A100
Simulation Throughput Comparison
steps / s
TRACEOpenMM + PLUMED
Alanine
439 atomsTRACE5,529 steps/s
OpenMM + PLUMED125 steps/s
Chignolin
2,333 atomsTRACE5,293 steps/s
OpenMM + PLUMED124 steps/s
DHFR
23,558 atomsTRACE2,157 steps/s
OpenMM + PLUMED90 steps/s
ApoA1
92,224 atomsTRACE786 steps/s
OpenMM + PLUMED93 steps/s
| System | Atom count | TRACE (steps/s) | OpenMM + PLUMED (steps/s) | Speedup factor | Force difference (eV/Å) |
|---|---|---|---|---|---|
| Alanine | 439 | 5,529 | 125 | 44× | 4.6×10⁻⁷ |
| Chignolin | 2,333 | 5,293 | 124 | 43× | 1.6×10⁻⁷ |
| DHFR | 23,558 | 2,157 | 90 | 24× | 1.2×10⁻⁶ |
| ApoA1 | 92,224 | 786 | 93 | 8.4× | 8.7×10⁻⁸ |