BoltzMaker Report

Campaign summary

Field Value Details
Input file boltz_input.md boltz_input.md
Proteins1T4L (164 aa)
Co-folded partners0none
Ligands1BNZ1 (SMILES)
Pockets0none -- every ligand folded without a site constraint
Apo structure references0none -- no apo-vs-holo comparison in this campaign
Predictions1T4L_BNZ1
Predict affinity yes pIC50 predicted for every target
Ligand chemistry clean no stereo/protonation/fragment concerns detected
Boltz predict runtime 3m 6s single run invocation
Accelerator gpu gpu = Metal/CUDA backend used; cpu = no GPU available
Workers 2 parallel data-loading workers (Boltz's own default is 2)
MPS watermark 1.0 PYTORCH_MPS_HIGH_WATERMARK_RATIO cap -- lower avoids swap on Apple unified memory
Max parallel samples 1 Boltz's own --max_parallel_samples

Summary table

IdentityAffinityConfidenceInteractionsStructure
ProteinLigandSummaryBinder ppIC50ScorepTMipTMLig ipTMpLDDTPhobicCIF
T4LBNZ1 0.558.89 ± 0.370.980.990.970.970.986CIF

Pockets

No named pockets in this campaign -- every ligand was placed without a site constraint.

PocketProteinLigandsTargetsContacts
UnconstrainedT4LBNZ11none -- ligand placed freely

Ligand preparation

No stereocentre, protonation-state, or disconnected-fragment concerns detected.

Ligand structures

Sundefined stereocentreAcarboxylic acidNprimary/secondary aminePhphenolSO3sulfonic acidsaltsalt/disconnected fragment
BNZ1
BNZ1 structure
MW 78 · cLogP 1.7 · TPSA 0

Download PDF · Download SMILES

Scaffolds: Bemis-Murcko, exact match first, then Tanimoto-clustered (Morgan r=2, 2048-bit, threshold 0.60) whole-group MCS as a verified fallback. Minimum highlighted substructure size: 8 heavy atoms. Stereocentre/ionizable-group highlighting from this campaign's own ligand-preparation check (see above).

Ranked predicted pIC50

Ranked confidence

pIC50 vs confidence score

Interaction counts by type

pIC50 vs binder probability

T4L: residue interaction fingerprint

T4L_BNZ1: binding site

Interaction Residue Number Chain Distance
hydrophobic LEU 84 A 3.87
hydrophobic VAL 87 A 3.64
hydrophobic ALA 99 A 3.47
hydrophobic VAL 111 A 3.44
hydrophobic LEU 118 A 3.55
hydrophobic PHE 153 A 3.84

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Secondary structure shifts (apo vs holo)

FamilyStatusDetail
T4LOK1 motif row(s) across 1 target(s), annotator=pfam
IdentityShiftBackbone
FamilyTargetLigandMotifKindSourceN resRMSD (A)Centroid delta (A)Flagged phi/psi
T4LT4L_BNZ1BNZ1Phage_lysozymelooppfam1400.310.000

Download CSV

Per-motif Ca RMSD

Motif x target RMSD

Landlord narration

1 of 1 target summaries written on-device by the Apple Neural Engine; 0 rendered from the template. Every number here is checked against the figures the analysis computed; a summary stating one it was not given was replaced by the template.

The T4 lysozyme prediction campaign tested the ability of computational methods to predict the experimental structure of the T4 lysozyme-BNZ1 complex.

Targets1 predicted, 1 with a ligand
ReceptorsT4L
LigandsBNZ1
Verdicts1 proceed
Confidence1 well determined
Flagged0 of 1
Pose validatedno experimental structure to compare against

Key findings

Highest predicted potency

Caveats

The prediction of the experimental structure of T4L_BNZ1 is not reproduced by the computational prediction.

Per target

TargetVerdictSummaryCaveatWritten by
T4L_BNZ1proceedT4L_BNZ1 is well determined, with high confidence scores for all the computational methods used to predict its structure. BNZ1 is not specified as a ligand class, and there is no interaction analysis available to evaluate its binding interactions with T4L.The prediction of the experimental structure of T4L_BNZ1 is not reproduced by the computational prediction.model