t4_lysozyme · BoltzMaker

t4_lysozyme packed 2026-08-13

1 Proteins

0 Co-folded partners

1 Ligands

0 Pockets

0 Apo structure references

1 Predictions

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Campaign summary

Field	Value	Details
Input file	boltz_input.md	boltz_input.md
Proteins	1	T4L (164 aa)
Co-folded partners	0	none
Ligands	1	BNZ1 (SMILES)
Pockets	0	none -- every ligand folded without a site constraint
Apo structure references	0	none -- no apo-vs-holo comparison in this campaign
Predictions	1	T4L_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

pIC50 vs confidence score

Click a point to open that target, in the panel below the Targets table.

pIC50 vs binder probability

Click a point to open that target, in the panel below the Targets table.

Ranked predicted pIC50

Click a point to open that target, in the panel below the Targets table.

Ranked confidence

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Summary table

Identity			Affinity		Confidence					Interactions	Structure
Protein	Ligand	Summary	Binder	pIC50	Score	pTM	ipTM	Lig	pLDDT	Phob	CIF
T4L	BNZ1		0.55	8.89 ± 0.37	0.98	0.99	0.97	0.97	0.98	6	CIF

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🎯 affinity Likely binder (p ≥ 0.7) Uncertain (0.3-0.7) Likely non-binder (p < 0.3)

🛡️ confidence High confidence (≥ 0.7) Moderate confidence (0.5-0.7) Low confidence (< 0.5)

Predictions

One row per prediction. Click one to see its pose and interactions, in the panel below.

Flagged only

Run	Prediction	Protein	Ligand	Pocket	Class	Confidence	pIC50	Interactions	Flags

Target

Overall structure

Interaction diagram

Detected interactions

Metrics

Ligand pose

Superposed targets

Sequence

Pockets

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

Pocket	Protein	Ligands	Targets	Contacts
Unconstrained	T4L	BNZ1	1	none -- ligand placed freely

Where the ligands landed

Ligand preparation

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

Ligand structures

Sundefined stereocentreAcarboxylic acidNprimary/secondary aminePhphenolSO3sulfonic acidsaltsalt/disconnected fragment

BNZ1

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).

Interaction counts by type

Click a point to open that target, in the panel below the Targets table.

SSE motif shifts (apo vs holo)

Identity						Shift			Backbone
Family	Target	Ligand	Motif	Kind	Source	N res	RMSD (A)	Centroid delta (A)	Flagged phi/psi
T4L	T4L_BNZ1	BNZ1	Phage_lysozyme	loop	pfam	140	0.31	0.00	0

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Family coverage and SSE shifts

Family	Status	Detail
T4L	OK	1 motif row(s) across 1 target(s), annotator=pfam

Overall shift statistics

1 target(s), 1 motif(s) compared
Mean Ca RMSD: 0.31 A (median 0.31 A) — largest shift: 0.31 A at T4L_BNZ1 / Phage_lysozyme
Mean centroid shift: 0.00 A
Flagged phi/psi outlier residues: 0
Kinase state changes detected: 0 DFG, 0 alphaC

Per-motif Ca RMSD

Loops

Transmembrane

Motif x target RMSD

Residue interaction fingerprints

Which residues each ligand touches, per protein. One scale for all of them, so a strong contact looks the same in every plot.

T4L

The reports as files

The same panels as BoltzMaker wrote them, if you want the whole page in one file.

Full dashboard (5.4 MB) Secondary structure (apo vs holo) (4.4 MB)

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.

Targets	1 predicted, 1 with a ligand
Receptors	T4L
Ligands	BNZ1
Verdicts	1 proceed
Confidence	1 well determined
Flagged	0 of 1
Pose validated	no experimental structure to compare against

Key findings

Of 1 targets, 1 are marked proceed, 0 caution and 0 discard.
1 of 1 targets are well determined; 0 are not.

Highest predicted potency

BNZ1 on T4L_BNZ1, predicted pIC50 8.89

Caveats

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

Per target

Target	Verdict	Summary	Caveat	Written by
`T4L_BNZ1`	proceed	T4L_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