Submission 8 | Proteinbase

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Submission 8 | Proteinbase

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eputnam/Submission 8

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Submitted toNipah Binder Competition

Description

Protein-Hunter Boltz-2 hallucination pipeline -> target epitopes (taken from contact points between glycoprotein and receptor/antibodies/PeSTo prediction of binding sites) + non-contact epitope potentials (location of glycosylated residues) (distance thresholds relaxed in the beginning, but more stringent for final designs)
ESMFold structure re-prediction filter (rough "inverse-folding" model, using the assumption that if plddt was high and RMSD between boltz-2 structure and ESMfold structure was less than 3A, then the structure is probably correct)
Rosetta filtering (from protein-hunter pipeline) + PRODIGY scoring for binding affinity
Boltz-2 re-prediction with higher number of recycles and diffusion steps + ipSAE_min scoring on the predicted structure
Final check for solubility and usablity
Ran optional optimization steps with template and binder sequence to improve design (repeat steps 1-5 with more stringent thresholding)

Proteins (8)

TableGrid

id: soft-seal-frost

Binder

Miniprotein

Protein-Hunter

soft-seal-frost

Nipah Virus Glycoprotein G

None

60.60

True

7.0 kDa

64

id: golden-seal-thorn

Binder

Other

Protein-Hunter

golden-seal-thorn

Nipah Virus Glycoprotein G

None

87.75

True

10.6 kDa

101

id: pale-wolf-oak

Binder

Miniprotein

Protein-Hunter

pale-wolf-oak

Nipah Virus Glycoprotein G

None

83.58

True

6.9 kDa

64

id: vast-bee-sand

Binder

Miniprotein

Protein-Hunter

vast-bee-sand

Nipah Virus Glycoprotein G

None

85.37

True

7.1 kDa

64

id: quick-lion-pearl

Binder

Other

Protein-Hunter

quick-lion-pearl

Nipah Virus Glycoprotein G

None

86.48

True

10.9 kDa

101

id: crimson-heron-snow

Binder

Other

Protein-Hunter

crimson-heron-snow

Nipah Virus Glycoprotein G

None

86.91

True

10.8 kDa

101

id: lunar-toad-bronze

Binder

Other

Protein-Hunter

lunar-toad-bronze

Nipah Virus Glycoprotein G

0.71

86.78

--

11.0 kDa

101

id: rough-bison-ivy

Binder

Other

Protein-Hunter

rough-bison-ivy

Nipah Virus Glycoprotein G

0.87

86.94

--

10.7 kDa

101

Rows per page

1-8 of 8

About

8proteins designed

8proteins validated

75%expression rate

0.81Avg ipSAE

Design Methods

EProtein-Hunter8

Targets

Nipah Virus Glycoprotein G

0 binders•-- avg KD

Design Class

other 63%

miniprotein 38%

Binding Strength

none 75%

unknown 25%

Expressed

true 75%

unknown 25%

De Novo

yes 75%

unknown 25%

Classification

mainly Alpha 100%

Architecture

unknown 100%