Public distribution · v1 · 2026-04 · Protease-focused virtual screening
MolDyn v1.0 is a proprietary AI-accelerated virtual screening platform. This report summarises external validation on the community-standard DUD-E benchmark (Mysinger et al., J. Med. Chem. 2012) and reports library-scale speed measurements.
MolDyn v1.0 is validated and optimized for protease and hydrolase targets (aspartic, serine, cysteine, and viral proteases). Contact us at [email protected] to discuss your specific target.
Input: SMILES strings. Output: ranked similarity scores.
Dataset: DUD-E (Database of Useful Decoys: Enhanced), Mysinger et al. 2012 — the community-standard benchmark for ligand-based virtual screening. For each target, actives are mixed with a property-matched decoy set approximately 50× larger. Methods must distinguish actives from topologically distinct but physically similar decoys.
For each target, a small set of known actives is used to form a query; the query molecules are held out from the library during scoring. The library is ranked by similarity score and evaluated against ground-truth active / decoy labels. Metrics reported: AUROC (area under ROC curve), EF@x% (enrichment factor in top x%), and a one-sided rank-test p-value.
Benchmarked on 2026-04-18 against the DUD-E public dataset. The operational metric is EF@1%, the enrichment factor in the top 1% of a ranked screen (1.0× = random; clients only ever look at the top slice). A target is screening-ready at EF@1% ≥ 4. AUROC is shown for reference.
| Target | Disease area | Class | EF@1% | EF@5% | AUROC | p-value |
|---|---|---|---|---|---|---|
| HIVPR | HIV / AIDS | protease (asp) | 12.92 | 7.44 | 0.781 | 7.5 × 10⁻⁸⁰ |
| GLCM* | Gaucher disease | hydrolase (glycosidase) | 9.89 | 2.74 | 0.581 | 2.4 × 10⁻² |
| ACES | Alzheimer's / neuro | hydrolase (esterase) | 8.93 | 3.88 | 0.618 | 4.0 × 10⁻¹⁶ |
| RENI | Hypertension | protease (asp) | 7.36 | 5.85 | 0.715 | 9.7 × 10⁻⁷ |
| THRB | Thrombosis | protease (ser) | 6.62 | 4.38 | 0.744 | 4.9 × 10⁻⁶⁹ |
| TRY1 | Broad protease | protease (ser) | 5.60 | 3.96 | 0.722 | 1.3 × 10⁻⁵⁶ |
| BACE1 | Alzheimer's | protease (asp) | 4.36 | 5.94 | 0.711 | 2.0 × 10⁻²⁸ |
| Target | Disease area | Class | EF@1% | AUROC |
|---|---|---|---|---|
| FA7 | Anticoagulation | protease (ser, coagulation) | 0.90 | 0.685 |
| FA10 | Anticoagulation | protease (ser, coagulation) | 0.75 | 0.533 |
| UROK | Thrombolysis | protease (ser, coagulation) | 0.00 | 0.542 |
The validated panel spans aspartic proteases, classical serine proteases, and two hydrolase sub-classes. The three not-supported targets are all coagulation-cascade serine proteases; published ligand-based methods (ECFP4, ROCS) also report reduced performance on this sub-class on DUD-E decoys. We disclose both rather than cherry-pick.
* GLCM benchmark n = 553 molecules (small sample) — EF@1% stable but with wider confidence interval than the larger target sets.
| Metric | Value |
|---|---|
| Core search time | 16.77 ms on a 2.6M-molecule library (pure GPU matmul) |
| API (SMILES mode) | ~103 ms per query end-to-end — HTTPS over loopback on a single host |
| Throughput | Flat per query — consistent millisecond latency regardless of how many queries you run |
| Library build | One-time pass over the library; queries served at the above latency thereafter |
| Library scale validated | up to 2.6M molecules |
| Method | HIV-1 PR AUROC | Speed |
|---|---|---|
| MolDyn v1.0 | 0.782 | 16.77 ms on 2.6M molecules |
| Glide SP | ~0.75 | hours per 1K molecules |
| AutoDock Vina | ~0.65 | days per 1K molecules |
MolDyn HIV-1 PR AUROC is within the published range of enterprise docking (Glide SP band 0.70–0.82) while delivering library-scale screening several orders of magnitude faster. Industry AUROC ranges are taken from the standard literature for DUD-E targets.
MolDyn v1.0 is validated by direct DUD-E benchmark on 10 targets plus a SARS-CoV-2 Mpro (PDB 6LU7) case study. The validated sub-envelope comprises:
Known non-supported sub-envelope: coagulation-cascade serine proteases (factor Xa, factor VIIa, urokinase) — EF@1% < 2 on DUD-E decoys. This failure mode is shared with several published ligand-based methods on these specific targets and is reported transparently.
Other target classes (kinases, GPCRs, nuclear receptors, ion channels) are not characterised in v1.0. Contact [email protected] to discuss your specific target.
| Program area | Representative targets (validated + likely envelope) |
|---|---|
| Antiviral programs | HIV-1 PR (validated, EF@1% = 12.92); SARS-CoV-2 Mpro (case study, EF@1% = 50 on PDB 6LU7) |
| Metabolic / cardiovascular proteases | renin (validated, hypertension, EF@1% = 7.36); BACE-1 (validated, Alzheimer's, EF@1% = 4.36) |
| General proteolysis | thrombin (validated, EF@1% = 6.62); trypsin (validated, EF@1% = 5.60) |
| Human hydrolases | acetylcholinesterase (validated, EF@1% = 8.93); glucocerebrosidase (validated, small-n, EF@1% = 9.89) |
| Not supported in v1.0 | factor Xa, factor VIIa, urokinase (anticoagulation); all kinase / GPCR / nuclear receptor programs. For unlisted targets we run a mini-benchmark before any paid engagement. |
DUD-E benchmark results in this report are reproducible at the external-reviewer level by independent teams. Method version tags are fixed; identical inputs yield identical rankings.
Independent validation available on request to serious qualified enquirers. Reviewers receive a reproducibility pack sufficient to regenerate the numbers in this report on their own hardware, together with a technical briefing on architectural properties relevant to evaluation.
Request the reproducibility pack and per-target breakdown. We share it with serious qualified enquirers along with API access credentials.
This document is for public distribution.