🧬 PRISM Protein Cage Designer

RFdiffusion2 backbone → LigandMPNN homo-oligomeric sequence → BindCraft interface optimisation

🔁 Design pipeline

RFdiffusion2 — SE(3) flow matching generates 200-residue subunit backbones
PRISM symmetry engine — 12-subunit T-cage at 50 Å radius
LigandMPNN — homo-oligomeric sequence design (identical chains)
BindCraft — AF2-hallucination glue-binder optimisation at A–C interface

📊 Run summary

Cage designs	4
Subunits / cage	12 (T symmetry)
Residues / subunit	200
Glue binders generated	11 (Design 0)
Relaxed binders	3
Best ΔG	−44.6 REU

🏗 Cage Assemblies

Design 0 — T‑cage

✅ 11 glue binders

Cage geometry
Cavity ø	6.7 nm
R_g	52.6 Å
Shell	33.4–69.6 Å
Close interfaces	6
Clashes (2 Å)	0
LigandMPNN sequence
Confidence	0.439
Seq recovery	0.305
Interface res	16

Chain A sequence (200 res):

VEREIRRAMERCLPDLLKAEVVVVILNGVDLDTQGEAFDILTRELVRAIREAKAANPDRKIHVLIAVSAALTCVRALREYGGRGGVERAAAKAAEVAAKMAAAFEAVGATTRTVVLTAATQAAVDYAEANPDASLDDILAVANAAAAGEIAAEAAAIIRA…

Design 1 — T‑cage

Binder pending

Cage geometry
Cavity ø	4.0 nm
R_g	54.0 Å
Shell	20.1–79.7 Å
Close interfaces	30
Clashes (2 Å)	0
LigandMPNN sequence
Confidence	0.388
Seq recovery	0.28
Interface res	26

Chain A sequence (200 res):

AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA…

Design 2 — T‑cage

Binder pending

Cage geometry
Cavity ø	6.4 nm
R_g	52.6 Å
Shell	32.0–67.7 Å
Close interfaces	6
Clashes (2 Å)	0
LigandMPNN sequence
Confidence	0.367
Seq recovery	0.265
Interface res	13

Chain A sequence (200 res):

RRQAEMLDIALAIMGAQLELALLKREDERAAARERMRAELERLFAEAGLAVANARAGMAATRVLRAPGTPAGVAALRAWWAARRAELRARAAATSGVLAACEAAAAVIEAQIRRARADEPREVSVEVILSDDFVTVVALSLPAEEHAERYGSLGFAVSIC…

Design 3 — T‑cage

Binder pending

Cage geometry
Cavity ø	4.4 nm
R_g	52.9 Å
Shell	22.1–71.2 Å
Close interfaces	0
Clashes (2 Å)	0
LigandMPNN sequence
Confidence	0.388
Seq recovery	0.14
Interface res	0

Chain A sequence (200 res):

LLEERRAAEAARRARRLAWLGRLGGAGGLVGALAVLKVYPLLGLLLLALVLYLLYLASLERDPLLAGIILGVAGVLGMLGGIAASGKLYGAKTTVEQAADGRWRATHTFEEMTPEEIEELKERMKEVLDRLEETGDVEEVKAEVLDSLKETDSAVEWGKA…

🧲 Glue Binder Analysis — Design 0 (A–C Interface)

Interface targeting: Hotspot residues 72–89, 124, 127 on the A–C subunit interface (contact distance <2.1 Å). BindCraft ran AF2 hallucination to design a peptide that bridges two adjacent cage subunits. iPTM < 0.5 indicates early-stage designs — these are initial trajectories; ΔG and shape complementarity are the primary quality filters.
Viewer shows the full 12-subunit cage (muted, rainbow chains A–L) with the designed glue binder (■ gold chain M) docked at the A–C interface.

l78_s706912

Relaxed

AF2 prediction quality
pLDDT	0.83
iPTM	0.15
Rosetta interface energy
ΔG (REU)	-25.3
dSASA (Å²)	712
Shape compl.	0.70
Structure
Length (res)	78
Interface res	9
Target RMSD	2.66

Binder sequence:

GTHTIEWEAFGMTLTYTFEPDEAGVMMVTMTVGETTLFTIAWQVYRAMMQFLMDTFPGWREFFGPHMPEMDAVHDDMM

l64_s708990

Relaxed

AF2 prediction quality
pLDDT	0.80
iPTM	0.16
Rosetta interface energy
ΔG (REU)	-44.6
dSASA (Å²)	1276
Shape compl.	0.75
Structure
Length (res)	64
Interface res	17
Target RMSD	1.33

Binder sequence:

SGQKEWFKMVKDWVDDMIGMFEKWQKHFASMGGNNTSKEVAKMVQVAIDGLKDLRSFLESQISG

l56_s204482

Relaxed

AF2 prediction quality
pLDDT	0.78
iPTM	0.16
Rosetta interface energy
ΔG (REU)	-24.1
dSASA (Å²)	1007
Shape compl.	0.63
Structure
Length (res)	56
Interface res	13
Target RMSD	0.80

Binder sequence:

MAPPDMTGMTPVQPVKEWKKWTMKVADQNGWPKSWKKMVENVFDQAYDNTKQMTGM

l53_s61545

LowConfidence

AF2 prediction quality
pLDDT	N/A
iPTM	N/A
Rosetta interface energy
ΔG (REU)	N/A
dSASA (Å²)	N/A
Shape compl.	N/A
Structure
Length (res)	53
Interface res	N/A
Target RMSD	N/A

l54_s426457

LowConfidence

AF2 prediction quality
pLDDT	N/A
iPTM	N/A
Rosetta interface energy
ΔG (REU)	N/A
dSASA (Å²)	N/A
Shape compl.	N/A
Structure
Length (res)	54
Interface res	N/A
Target RMSD	N/A

l57_s497434

LowConfidence

AF2 prediction quality
pLDDT	N/A
iPTM	N/A
Rosetta interface energy
ΔG (REU)	N/A
dSASA (Å²)	N/A
Shape compl.	N/A
Structure
Length (res)	57
Interface res	N/A
Target RMSD	N/A

l58_s717142

LowConfidence

AF2 prediction quality
pLDDT	N/A
iPTM	N/A
Rosetta interface energy
ΔG (REU)	N/A
dSASA (Å²)	N/A
Shape compl.	N/A
Structure
Length (res)	58
Interface res	N/A
Target RMSD	N/A

l66_s194391

LowConfidence

AF2 prediction quality
pLDDT	N/A
iPTM	N/A
Rosetta interface energy
ΔG (REU)	N/A
dSASA (Å²)	N/A
Shape compl.	N/A
Structure
Length (res)	66
Interface res	N/A
Target RMSD	N/A

l70_s495959

LowConfidence

AF2 prediction quality
pLDDT	N/A
iPTM	N/A
Rosetta interface energy
ΔG (REU)	N/A
dSASA (Å²)	N/A
Shape compl.	N/A
Structure
Length (res)	70
Interface res	N/A
Target RMSD	N/A

l77_s504296

LowConfidence

AF2 prediction quality
pLDDT	N/A
iPTM	N/A
Rosetta interface energy
ΔG (REU)	N/A
dSASA (Å²)	N/A
Shape compl.	N/A
Structure
Length (res)	77
Interface res	N/A
Target RMSD	N/A

l77_s997363

LowConfidence

AF2 prediction quality
pLDDT	N/A
iPTM	N/A
Rosetta interface energy
ΔG (REU)	N/A
dSASA (Å²)	N/A
Shape compl.	N/A
Structure
Length (res)	77
Interface res	N/A
Target RMSD	N/A