Submission 1

Description

I used my custom version of BindCraft modified such that you can give a partial structure as input and added an ipSAE loss that was up-weighted compared to the other losses. As input I used a known nanobody scaffold (https://www.nature.com/articles/s41594-018-0028-6), and allowed only the CDR loops to be redesigned. The starting structure was based on the placement of an existing Hemagglutinin-neuraminidase antibody binder (PDB: 8TQI) where only the heavy chain is in contact with the viral protein, making it more nanobody-like. The Nipah target protein was heavily truncated for more efficient iterations.

Proteins (10)

TableGrid

Ooceane.follonier

id: shy-cobra-sand

Binder

Nanobody

BindCraft, modified for partial binder design, with ipSAE loss

Target

Nipah Virus Glycoprotein G

0.76

82.27

14.2 kDa

129

id: misty-panther-quartz

Binder

Nanobody

BindCraft, modified for partial binder design, with ipSAE loss

Target

Nipah Virus Glycoprotein G

0.73

83.23

14.0 kDa

129

id: soft-bear-iron

Binder

Nanobody

BindCraft, modified for partial binder design, with ipSAE loss

Target

Nipah Virus Glycoprotein G

0.57

80.12

14.3 kDa

129

id: silver-falcon-orchid

Binder

Nanobody

BindCraft, modified for partial binder design, with ipSAE loss

Target

Nipah Virus Glycoprotein G

0.53

81.28

14.1 kDa

129

id: deep-tiger-ash

Binder

Nanobody

BindCraft, modified for partial binder design, with ipSAE loss

Target

Nipah Virus Glycoprotein G

0.51

85.34

14.1 kDa

129

id: bright-panda-ruby

Binder

Nanobody

BindCraft, modified for partial binder design, with ipSAE loss

Target

Nipah Virus Glycoprotein G

0.35

79.90

14.4 kDa

129

id: jade-cobra-fern

Binder

Nanobody

BindCraft, modified for partial binder design, with ipSAE loss

Target

Nipah Virus Glycoprotein G

0.27

81.43

14.1 kDa

129

id: small-moth-jade

Binder

Nanobody

BindCraft, modified for partial binder design, with ipSAE loss

Target

Nipah Virus Glycoprotein G

0.16

80.28

14.4 kDa

129

id: jade-jaguar-bronze

Binder

Nanobody

BindCraft, modified for partial binder design, with ipSAE loss

Target

Nipah Virus Glycoprotein G

0.00

79.84

14.4 kDa

129

id: small-ox-rose

Binder

Nanobody

BindCraft, modified for partial binder design, with ipSAE loss

Target

Nipah Virus Glycoprotein G

0.00

80.55

14.2 kDa

129