--- license: cc-by-4.0 tags: - structure-prediction - protein-ligand - zika - openbind-challenge --- # OpenBind Blind Challenge 1 — Method Report **Track:** Structure Prediction **Target:** Zika virus NS2B-NS3 protease **Compounds:** 400 / 400 submitted --- ## Summary Poses were generated by **MCS-guided template transfer followed by protein-aware constrained minimisation**. No GPU was used for the submitted poses. Co-folding (Boltz-2, OpenFold3) was evaluated and rejected on measured performance; its results are reported below as negative findings. The method is conditional rather than general: where a close structural analogue exists among deposited ZIKV protease complexes it is accurate, and where one does not it fails. That bimodality is quantified below rather than averaged away. ## Pipeline 1. **Receptor ensemble.** All ZIKV NS2B-NS3 entries were retrieved from the RCSB by sequence search on the 168-residue NS3 construct and superposed on 29HN (apo, closed, 1.774 A, P4(3)22 — the challenge crystal form) by NS3 Calpha, with residue correspondence established by sequence alignment rather than residue number. 195 of 200 members superposed within 1.0 A (median Calpha RMSD 0.253 A). The pocket has one meaningful degree of freedom, a bimodal Tyr161 rotamer, so two receptors are carried: 7H1Z (majority rotamer) and 7HOQ (minority). 2. **Template library.** 129 orthosteric ligand poses extracted in the common frame, disjoint from the validation set. Peptidomimetics, covalent adducts and macrocycles were excluded as unrepresentative of the blinded compound set. 3. **Template selection.** For each compound, an ECFP4 prefilter over the library followed by `rdFMCS` (ringMatchesRingOnly, completeRingsOnly, CompareElements / CompareOrderExact). The donor maximising **MCS coverage** — matched atoms divided by query heavy atoms — is chosen. 4. **Pose transfer.** Constrained embedding (ETKDGv3 with `coordMap`) pins the MCS atoms onto the donor's crystallographic coordinates; MMFF relaxation with position constraints on the pinned atoms completes the remainder. Pinned atoms land a median 0.002 A from their template positions. 5. **Protein-aware minimisation.** The MMFF relaxation above has no protein term, so peripheral atoms are drawn back into the receptor. Every protein heavy atom within 6 A is added to the force field as a fixed extra point and flat-bottom distance restraints push any too-close pair out to 0.80 x (sum of van der Waals radii), while MCS atoms are held to 0.30 A of slack. Median displacement 0.32 A. 6. **Assembly.** Receptor chains A (NS2B) and B (NS3) plus the ligand as a single `LIG` residue in chain C, waters stripped, explicit CONECT records. The receptor is chosen per compound to match the donor's Tyr161 rotamer. ## Validation Tuning and evaluation used a **held-out benchmark of 41 public ZIKV NS2B-NS3 holo structures**, disjoint from the template library, scored with OpenStructure (`SCRMSDScorer`, `LDDTPLIScorer`) and PoseBusters under the challenge's conjunction: BiSyRMSD < 1.5 A **and** lDDT-PLI > 0.8 **and** all PoseBusters checks. No leaderboard feedback was used at any point. A calibration of the three gates under rigid displacement showed that **lDDT-PLI binds before BiSyRMSD**: at 1.25 A displacement the RMSD gate still passes 100% while lDDT-PLI passes about a third. The effective accuracy requirement is nearer 1.1 A than the nominal 1.5 A. ### Head-to-head, 41-complex benchmark | method | passes all three gates | |---|---| | Boltz-2, rank-0 sample | 24.4% | | Boltz-2, oracle over 5 samples | 34.1% | | Boltz-2 with pocket restraints | 19.5% | | Template transfer | 34.1% | | **Template transfer + protein-aware minimisation** | **39.0%** | Boltz-2's 34.1% requires selecting the correct sample out of five, which its confidence score does not support (Spearman -0.59 against RMSD). The template method emits one pose, so its figure needs no selector. ### Performance is conditional on template precedent | MCS coverage | benchmark pass rate | compounds in this submission | |---|---|---| | >= 0.8 | 88% (15/17) | 220 | | 0.6 - 0.8 | 9% | 116 | | < 0.6 | 0% | 64 | MCS coverage is a usable *a priori* selector (Spearman -0.80 against BiSyRMSD), known before any compute is committed. Median coverage across the submission is 0.818. ## Negative results Reported because they constrain what the remaining gap is, not as asides. - **Pocket restraints degrade co-folding.** A paired run (identical seed and inputs; the unrestrained YAML is a strict text prefix of the restrained one) restraining the ligand to within 6 A of 25 pocket residues moved Boltz-2 from 25.9% to 19.0%. `minimum_distance_to_protein` failures rose from 44 to 69 of 205 models: the restraint drives the ligand too deep. - **Co-folding does not complement template transfer.** Stratified by MCS coverage, Boltz-2's oracle is 18% below 0.8 and 59% above it — the same compounds are hard for both. A hybrid adds little. - **Free docking is the worst option tested.** On the 22 low-coverage benchmark complexes, smina produced 0/22, scoring zero on *both* accuracy gates with a PoseBusters pass rate of 31.8%, against 4.5% and 54.5% for template transfer. - **Anchored search** (MCS core pinned, 60 conformers of the remainder ranked by the smina scoring function) gave 2/22 versus 1/22 — a sound mechanism but not a solution at this sample size. ## Limitations - Roughly 180 of the 400 compounds fall below 0.8 MCS coverage, where no method tested here exceeds ~10%. They are chemically novel rather than small (median 23-25 heavy atoms, Tanimoto 0.25-0.46 to their nearest donor). - 56% of benchmark poses still exceed the 1.5 A RMSD gate after minimisation; the method is not generally accurate. - Minimised poses remain less physically clean than co-folded ones (PoseBusters 71.8% versus 78.1% for plain Boltz-2). - The improvement from minimisation (+2 compounds of 39) is not statistically significant on its own (paired exact test, p = 0.25); it is adopted on mechanism and on the absence of any regression, not on the delta. - Performance depends on an unusually dense structural prior for this target (196 liganded entries, one dominant crystal form, a rigid pocket). It would not transfer to a target with few co-crystals. ## Data and code declarations - **Proprietary data: none.** Every structure used is a public RCSB deposition and every compound SMILES came from the challenge distribution. - **Training data leakage:** not applicable to the submitted poses, which come from template transfer rather than a learned model. For the co-folding comparisons, benchmark structures were checked against each engine's training cutoff by *deposition* date (the conservative choice); all 42 fall outside the Chai-1, AF3 and OpenFold3 windows. Benchmark co-folding runs used `--use-templates false` to prevent inference-time retrieval of the reference structures. - **Software:** RDKit, OpenStructure, PoseBusters, gemmi, smina, Boltz-2 (v2.2.1), OpenFold3-preview — all open source.