Blame for README.md

---
license: cc-by-4.0
language:
  - en
tags:
  - chemistry
  - drug-discovery
  - structural-biology
  - protein-ligand
  - pose-prediction
  - co-folding
  - zika-virus
  - openbind
pretty_name: OpenBind Blind Challenge 1 Method Report (KR LAB Bio)
---

# Zika NS2B-NS3 Protease Complexes from Same-Campaign Templates, Docking and Co-Folding, with Consensus-Based Pose Selection

**OpenBind Blind Challenge 1 - Method Report**
Structure prediction track · Leaderboard alias **KR LAB Bio** · KR LAB Bio Inc., Republic of Korea
Draft v1, 2026-11-06. Describes the submission currently on the leaderboard (internal label v18).
No proprietary data was used. No test-set structures or labels were used at any step.

---

## 1. Summary

We predicted all 400 blinded NS2B-NS3/ligand complexes with two independent pose generators
and one selection procedure.

- **Pipeline A, template transplantation plus docking.** Every public Zika NS2B-NS3 crystal
  structure (294 PDB entries) was superposed onto the 29HN binding site. For each challenge
  ligand, the maximum common substructure with the closest template ligands was placed on the
  template's experimental coordinates, the rest of the molecule was built and relaxed, and the
  template's own protein was used as the receptor. Exhaustive docking and gnina CNN rescoring
  and refinement added candidates. A fixed rule selected one pose per ligand from a median of
  66 candidates, using spatial consensus between independent templates, recovery of the
  template contact pattern and the gnina CNN rank.
- **Pipeline B, co-folding.** Protenix (`protenix_base_20250630_v1.0.0`, training cutoff
  2025-06-30, no fine-tuning) produced 10 samples per ligand (2 seeds × 5 diffusion samples).
  The representative sample is the stereochemically correct sample around which most other
  samples cluster.
- **Assembly.** The co-folding representative was used whenever it passed all 22 PoseBusters
  checks (337 ligands). The remaining 63 ligands (39 with no stereochemically correct sample,
  24 that failed PoseBusters) used the Pipeline A selection.

Live leaderboard result (about 200 of the 400 compounds, collected 2026-11-06 11:34 UTC):

| Metric | Value |
|---|---|
| Success rate | **68.5%** (137 of 200) |
| BiSyRMSD < 1.5 Å | 137 |
| lDDT-PLI > 0.8 | 155 |
| PoseBusters pass | 200 / 200 |
| Mean BiSyRMSD | 1.70 Å |
| Mean lDDT-PLI | 0.837 |

Four findings account for most of the work:

1. **The public record already contains this chemical series.** 369 of the 400 challenge
   ligands share at least half of their heavy atoms with a ligand in a public structure
   (median MCS coverage 0.833), and 391 of the 400 closest templates come from the same
   crystal form (P4<sub>3</sub>2<sub>2</sub>) as the challenge. Template transplantation is
   therefore a strong baseline on its own.
2. **Within our own candidate set, selection plateaued.** Three successive changes to the
   selection rule (sections 4 and 7) each improved a leave-one-compound-out backtest, yet the
   live BiSyRMSD pass count stayed at 133 for all three submissions.
3. **Co-folding broke that plateau without fine-tuning.** Replacing the selected pose by the
   co-folding representative wherever it passed PoseBusters raised the live BiSyRMSD pass
   count from 133 to 137 and the mean BiSyRMSD from 1.84 Å to 1.70 Å. On 24 structures
   released after the model's training cutoff, the co-folding representative was within 1.5 Å
   for 9 ligands against 5 for Pipeline A.
4. **Backtest gains did not transfer to the live set.** A selection rule that won 11 of 12
   honest holdout splits by +5.2 percentage points moved the live score by +0.5 points. We
   explain why in section 7, and we have stopped treating backtest gains alone as evidence of
   improvement.

Negative results are listed in section 9: the levers we tested on the Pipeline A side, each
with the measurement that closed it.

---

## 2. Target, inputs and public data

- **Construct.** NS2B cofactor (chain A, 46 residues) and NS3 protease domain (chain B,
  168 residues) as given in `NS2B-NS3_protein_sequence.fasta`. The ligand is a single residue
  `LIG`. Every submitted file has three chains or fewer.
- **Reference frame.** The apo structure 29HN. 8PN6, named in the dataset README, is the same
  construct in the same space group. All coordinates in this work are expressed in the 29HN
  frame.
- **Public structures.** An RCSB full-text search for Zika NS2B-NS3 returned 294 entries
  (2026-10-23; the same query on 2026-10-28 returned no entries released after 2026-10-01).
  From these we extracted **209 ligand instances from 176 entries (174 distinct chemical
  components)**. Bonds and bond orders were taken from the PDB Chemical Component Dictionary
  by atom name rather than inferred from coordinates, which recovered 43 ligands that
  coordinate-based perception had broken.
- **Challenge ligands.** 400 SMILES, 9 to 36 heavy atoms, median 23; 77.2% have 20 or more
  heavy atoms.

No proprietary or unpublished data was used. The challenge's own crystal structures were never
available to us.

---

## 3. Pipeline A: candidate generation

### 3.1 Binding-site superposition

Each public structure was superposed onto 29HN using backbone atoms within 12 Å of the centre
of the catalytic triad (Kabsch). The evaluation superposes binding sites before computing
ligand RMSD, so a binding-site fit is the relevant one. When chain identification by triad
numbering failed, a residue-number offset was found by sequence alignment and the fit was
repeated. Median fit RMSD: 0.15 Å.

### 3.2 Template matching and transplantation

1. Morgan fingerprints shortlist templates; the MCS (rings match rings, complete rings only)
   ranks them by the number of shared heavy atoms. Up to four templates per ligand are kept
   (397 of 400 ligands have four).
2. Because of molecular symmetry, an MCS admits several atom mappings. We enumerate them,
   rigidly align each to the template, and keep the geometrically consistent ones. Using only
   the first mapping returned by the matcher displaced poses by 4-5 Å; enumerating mappings
   reduced the MCS RMSD to 0.17 Å.
3. The common atoms are fixed at the template's experimental coordinates; the rest of the
   ligand is built with ETKDGv3 and relaxed with MMFF94 in three stages (common atoms fixed,
   then positionally restrained, then a looser restraint only if geometry is still broken).
4. The template's own crystal structure, trimmed to the two protease chains nearest the active
   site, is the receptor. Its side chains are already arranged around a closely related ligand.
5. smina (Vinardo) local minimisation against that receptor removes clashes while keeping bond
   lengths and angles as built.

### 3.3 Docking and CNN rescoring

- smina (Vinardo), 22 Å box on the active site, exhaustiveness 16, 9 modes, against the
  template receptors. Docking candidates matter: removing them lowered the backtest from
  58.1% to 48.0%, and to half in the lowest-similarity stratum.
- gnina 1.3.2: every candidate is rescored in place (`--score_only --cnn_scoring rescore`),
  and the 12 best-ranked candidates per ligand are additionally refined with `--minimize`
  (median movement 0.26 Å; all refined poses kept valid geometry).

### 3.4 Validity gate

Every candidate considered for submission passes two checks in order:

- a **PDB round trip** identical to the path of the official validator. PDB files carry no
  bond orders, so the reader perceives bonds from coordinates; a pose with a stretched ring can
  gain a bond and fail validation even after passing PoseBusters;
- **PoseBusters 0.6.5**, the official `redock` configuration minus the RMSD checks
  (22 checks), with the molecule built from the challenge SMILES in place of `mol_true`, so
  that formula, bonds, double-bond stereochemistry and tetrahedral chirality are checked
  against the input.

---

## 4. Pipeline A: pose selection

### 4.1 The rule

Each candidate gets a score; lower is better. Candidates are walked in score order and the
first one that passes the validity gate is selected.

| Term | Weight | Meaning |
|---|---|---|
| spatial consensus | 1.0 | fraction of the ligand's other candidates within 1.2 Å RMSD |
| cross-template consensus | 2.0 | the same fraction counted only over candidates derived from *other* templates |
| contact recovery | 1.0 | fraction of the residues commonly contacted by the template ligands (median 14-15 residues) that this pose also contacts |
| contact Jaccard | 0.5 | Jaccard index between the pose's contact set and that reference set |
| gnina CNNscore rank | 0.3 | rank within the ligand's candidates |

Signs are set so that more consensus and more contact recovery lower the score.
Cross-template consensus carries the most weight because templates come from independent
crystal structures: agreement between them is evidence that does not come from the scoring
function. The CNN term uses the within-ligand rank, because CNNscore ranges differ between
ligands and absolute values would let a few ligands dominate the rule.

### 4.2 Consensus nudge

After selection and validation, the selected pose alone is moved a quarter of the way toward
the atom-wise mean of the candidates within 3 Å, then relaxed with MMFF under a strong
positional restraint (force constant 200, tolerance 0.05 Å) and validated again; if it fails,
the unmoved pose is submitted. Median movement 0.14 Å, maximum 0.38 Å. In v18 this applies to
60 of the 63 ligands that use Pipeline A.

The order matters. Our first version nudged the top-ranked candidates before selection, which
inflated the consensus terms (the median spatial consensus of selected poses rose from 0.36 to
0.56) and reshuffled the selection. Selecting first and nudging only the selected pose keeps
the selection unchanged.

---

## 5. Pipeline B: co-folding

- **Model.** Protenix 2.0.0 with the `protenix_base_20250630_v1.0.0` checkpoint (training
  cutoff 2025-06-30). Not fine-tuned.
- **Inputs.** The two protease chains and the ligand SMILES. A single MSA, computed once with
  the Protenix MSA server, was reused for all inputs since the protein is identical.
- **Sampling.** Seeds 101 and 102, five diffusion samples each, ten samples per ligand
  (five for five ligands where the second seed returned no output). About 13 seconds per input
  and seed on one RTX 4090.
- **Conversion.** Each predicted complex is superposed onto the 29HN binding site after a
  sequence-derived renumbering (NS3 +9, NS2B +43). Ligand atoms are mapped to the SMILES atom
  order, and each sample is flagged for whether its stereochemistry matches the SMILES. The
  co-folded protein, in the 29HN frame and numbering, is kept as that sample's receptor.
- **Representative sample.** Among samples with correct stereochemistry, the one with the
  largest number of other samples within 2.0 Å symmetry-corrected RMSD. For the 337 ligands
  where it was used, the median fraction of all ten samples within 2.0 Å of it was 1.0.
- **Gate.** The representative must pass the same validity gate (section 3.4). If it fails, its
  geometry is corrected with a strongly restrained MMFF minimisation and retried; receptors are
  tried in the order co-folded protein, Pipeline A receptor, receptor of the nearest
  Pipeline A candidate, 29HN.

**On the training cutoff.** A 2025-06-30 cutoff covers 183 of the 209 public template
ligands. The challenge structures themselves are unpublished. This is the same situation as the
organisers' OpenBind-0 baseline, an OpenFold3 checkpoint with the same cutoff (64.5% on the live
leaderboard). We therefore measured co-folding against our own pipeline on structures released
after the cutoff (section 7.3).

---

## 6. The submitted assembly (v18)

| Source of submitted pose | Ligands |
|---|---|
| Co-folding representative | 337 |
| Pipeline A, no co-folding sample with correct stereochemistry | 39 |
| Pipeline A, co-folding representative failed PoseBusters | 24 |
| *of the 63 Pipeline A poses:* template transplant + smina | 39 |
| *of the 63:* docking | 22 |
| *of the 63:* template transplant, unminimised | 2 |

- PoseBusters 22 checks: 400 / 400.
- Official validator (`validation/structure_validation.py`, tutorial repository commit
  `1b34ec2`): valid, 0 errors, 400 files.

---

## 7. Validation and what it could and could not tell us

### 7.1 Backtest design

We had no access to challenge structures, so every design decision on the Pipeline A side was
measured on public complexes:

- **Leave-one-compound-out.** For each of 145 public complexes (one per chemical component,
  best resolution), every structure containing that component was removed from the template
  library before predicting its pose. 145 is the ceiling: of the 174 components, 28 have no
  remaining template with enough MCS overlap to produce any pose.
- **Challenge-distribution weighting.** The backtest set is dominated by fragments (40% below
  15 heavy atoms against 14.8% in the challenge), and leave-one-out makes templates more
  distant than in the challenge (median best Tanimoto 0.391 against 0.520). Unweighted, the
  backtest underestimated the first live score by 25 points. We weight backtest compounds by
  heavy-atom and similarity strata to match the challenge.
- **Honest holdout.** To estimate the optimism of choosing a rule on the same data used to
  score it, we split the 145 compounds in half twelve times, re-selected every distance,
  weight and criterion on one half, and scored on the other.

### 7.2 The selection rule: backtest against live

| Submission | Selection | Backtest (145, weighted) | Holdout, 12 splits | Live success | Live BiSyRMSD pass |
|---|---|---|---|---|---|
| v7 | gnina CNN rank only | 43.6% | 43.6% | 66.0% | 133 |
| v11 | rule of section 4.1 | 51.7% | 48.9% (wins 11 of 12) | 66.5% | 133 |
| v16 | v11 with a feature-reading defect fixed, plus nudge | see note | - | 66.5% | 133 |
| **v18** | co-folding where valid, v16 elsewhere | not measurable | - | **68.5%** | **137** |

Note on v16: the submission code had not been reading the template identity of each pose, so
the cross-template term (weight 2.0) was zero in every submission from v10 to v15 while the
rule had been fitted with it. Fixing this moved the backtest from 51.6% to 54.0% under a
counting that holds similarity strata fixed per compound, and moved the live score by zero.

Three explanations are compatible with these numbers and we cannot separate them:

1. **Resolution.** The live set is about 200 compounds; one compound is 0.5 points.
2. **Leave-one-out is harder than the challenge.** With close templates available, as in the
   challenge, the CNN rank alone already picks well (66.0% live), and consensus has less to
   add. The advantage of consensus appeared mainly where templates were distant.
3. **Weighting is incomplete.** Similarity-stratum weights were capped at 4.0.

After v11 we stopped treating a backtest gain alone as evidence of improvement, and we compare
methods by submitting whole versions and reading the change in the live score. We never changed
individual compounds to probe the live score, since the final ranking uses all 400.

### 7.3 Co-folding against Pipeline A

| Evaluation set | Pipeline A | Co-folding representative | Either | Both |
|---|---|---|---|---|
| 24 structures released after 2025-06-30 (2025-cutoff model; 17 of 24 are fragments) | 5 | **9** | 10 | 4 |
| 145-compound backtest (2021-09-30-cutoff model `protenix_base_default_v1.0.0`, which saw 22 of the 209 templates) | **63** | 49 | 79 | 33 |

Counts are ligands within 1.5 Å. The two pipelines succeed on different compounds: together they
would reach 79 of 145. We found no signal that tells, for a given compound, which one is right
when they disagree. Areas under the ROC curve for that decision were 0.66 for co-folding
self-consistency, 0.60 for ligand pLDDT, 0.58 for ranking score and ipTM, and 0.48-0.54 for the
Pipeline A consensus and contact terms. A conditional switching rule (switch only when
self-consistency is at least 0.6 and cross-template consensus is below 0.15) went from 5 to 8 on
the 24-structure set and from 63 to 60 on the 145-compound backtest.

The 2025-cutoff model on the challenge is a different situation from either set, because it was
trained on earlier structures from the same series. Only the live leaderboard could measure it,
which is why v18 uses co-folding unconditionally wherever it is valid.

---

## 8. Leaderboard history

| Version | Submitted (UTC) | Change | Success | BiSyRMSD pass | lDDT-PLI pass | Mean BiSyRMSD |
|---|---|---|---|---|---|---|
| v7 | 2026-10-26 06:30 | Pipeline A, gnina CNN rank selection | 66.0% | 133 | 149 | 1.84 Å |
| v11 | 2026-10-26 18:32 | selection rule of section 4.1 | 66.5% | 133 | 150 | 1.83 Å |
| v16 | 2026-10-28 11:48 | feature-reading fix, consensus nudge | 66.5% | 133 | 152 | 1.84 Å |
| **v18** | 2026-10-28 23:51 | co-folding where valid | **68.5%** | **137** | **155** | **1.70 Å** |

PoseBusters was 200 / 200 for every version.

---

## 9. What did not work

All measured on the weighted 145-compound backtest unless stated. The reference is the rule of
section 4.1 at 58.1% on the 120-compound set used at the time, or the value given in the row.

**Candidate generation**

| Tried | Result |
|---|---|
| Eight templates per ligand instead of four | 65% to 55% on the subset regenerated for this test. The ceiling stayed at 94%; candidates rose from 54 to 96 per ligand and distant templates formed spurious consensus |
| One, two or three templates | 49.5-51.9% |
| Filtering templates by MCS coverage | 54.1-56.1% |
| Docking at exhaustiveness 64 and 20 modes | 65% to 58%; same ceiling, more candidates dilute the selection |
| Removing docking candidates | 58.1% to 48.0% |
| Boltz-2 co-folding without fine-tuning (fragment probe) | 10.7%, below Pipeline A |

**Selection features**

| Tried | Result |
|---|---|
| Rescoring on several receptors (mean, minimum, affinity, VS score) | 46.7-55.5% |
| Burial of ligand atoms | 46.0% |
| Distance to the template-ligand hotspot | 43.1% |
| Hydrogen bonds, salt bridges, hydrophobic contacts (geometric definitions) | 41.4-51.1% |
| Ensemble score spread, template resolution, transplant shift, MCS RMSD | all harmful |
| Learned models on 32 features (logistic regression, gradient boosting, random forest) | 45.7-53.1% |
| Pairwise ranking with learned linear weights | 47.2% (learned order matched our rule) |

The physical and chemical terms separate correct from incorrect poses at the pose level (for
example 4 against 3 hydrogen bonds, 73 against 50 hydrophobic contacts) but lower the success
rate when added to the rule. Favouring more contacts selects over-buried poses; we read this as
the balance already being encoded in the gnina CNN.

**Selection procedure**

| Tried | Result |
|---|---|
| Weighting consensus by CNN score or contact recovery | 56.1-57.0% (plain counts are better) |
| Two-step selection (site first, then representative) | 47.4-50.0% |
| Medoid of the top candidates | 50.9-56.8% |
| Cross-template consensus counted over template families | 53.1-54.8% |
| Docking poses first for fragments (fewer than 18 heavy atoms) | 54.0% to 51.8% after the v16 fix |
| Co-folding samples as additional consensus votes (weights 0.5-8, radii 1.5-3 Å; 2021-cutoff model) | 53-59 of 145 ligands against 61 |

**Fragments remain the hardest class.** In our early 120-compound backtest, compounds below
18 heavy atoms succeeded at 9-29% against 50-71% above, although the best candidate is often within 0.3-0.8 Å. A
fragment has few contacts, and the same contacts are reproduced at several positions in the
pocket. This matches the live gap between lDDT-PLI passes (155) and BiSyRMSD passes (137).

---

## 10. Reproducibility and scope

| Component | Version |
|---|---|
| RDKit | 2026.09.1 |
| PoseBusters | 0.6.5 (same as the organisers' baseline reports) |
| smina | 2017.11.9 (Vinardo scoring) |
| gnina | 1.3.2 static release (`master:f23dd2b`) |
| Protenix | 2.0.0, checkpoint `protenix_base_20250630_v1.0.0` |
| Official validator and scoring code | `OpenADMET/OpenBind-Challenge-1-Tutorial` at commit `1b34ec2` |

**Compute.** Template transplantation, docking and selection ran on CPU nodes; gnina rescoring
and refinement on an 8 GB RTX 4060. Co-folding ran on one rented RTX 4090 for about eight hours,
at a cost of about USD 4.

**Code.** The code is not published at this time. This report is intended to describe every
step at a level that allows reimplementation with the public tools listed above. Parameters
not stated here were left at the tools' defaults.

**Data use.** Only public PDB entries, the challenge inputs and public model checkpoints were
used. No test-set structure, label or per-compound score entered any step. The live leaderboard
was used only to compare whole submissions.

---

## 11. Contact

KR LAB Bio Inc., Republic of Korea. Leaderboard alias: KR LAB Bio.