[GEM x Adaptyv: RBX1 Binder Design Competition] Submission 1 | Proteinbase

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[GEM x Adaptyv: RBX1 Binder Design Competition] Submission 1 | Proteinbase

M

Maksim Kuznetsov/[GEM x Adaptyv: RBX1 Binder Design Competition] Submission 1

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Submitted toGEM x Adaptyv: RBX1 Binder Design Competition

Description

For this competition, we train a text-only LLM that can operate on 3D protein structures by representing them efficiently in a textual format. We use LFM2-2.6b as a memory-efficient yet capable base model, which supports training and inference with the long textual contexts for handling 3D protein representations.

Full description of approach: https://drive.google.com/file/d/1VyqfJerlXkEiFRH4KrddHR1DIuRmSQag/view?usp=sharing

About

100proteins designed

7proteins validated

71%expression rate

Design Methods

MKLFM2-2.6B fine-tuned on peptide 3D structures100

Targets

RBX1

0 binders•-- avg KD

Design Class

unknown 94%

miniprotein 3%

peptide 3%

Binding Strength

unknown 93%

none 7%

Expressed

unknown 93%

true 5%

false 2%

De Novo

unknown 94%

yes 6%

Classification

unknown 96%

mainly Alpha 4%

Architecture

unknown 100%

Proteins (100)

TableGrid

MKMaksim Kuznetsov

id: silver-lynx-rose

Binder

Miniprotein

LFM2-2.6B fine-tuned on peptide 3D structures

silver-lynx-rose

RBX1

None

78.14

True

5.1 kDa

46

MKMaksim Kuznetsov

id: crimson-heron-ice

Binder

Peptide

LFM2-2.6B fine-tuned on peptide 3D structures

crimson-heron-ice

RBX1

None

46.96

True

6.2 kDa

53

MKMaksim Kuznetsov

id: radiant-heron-ruby

Binder

Peptide

LFM2-2.6B fine-tuned on peptide 3D structures

radiant-heron-ruby

RBX1

None

52.74

True

5.2 kDa

47

MKMaksim Kuznetsov

id: mellow-otter-frost

Binder

Miniprotein

LFM2-2.6B fine-tuned on peptide 3D structures

mellow-otter-frost

RBX1

None

54.23

False

7.8 kDa

65

MKMaksim Kuznetsov

id: wild-zebra-cloud

Binder

LFM2-2.6B fine-tuned on peptide 3D structures

No preview available

RBX1

None

--

True

--

48

MKMaksim Kuznetsov

id: azure-ibis-reed

Binder

Peptide

LFM2-2.6B fine-tuned on peptide 3D structures

azure-ibis-reed

RBX1

None

43.02

True

4.6 kDa

49

MKMaksim Kuznetsov

id: amber-vole-ash

Binder

Miniprotein

LFM2-2.6B fine-tuned on peptide 3D structures

amber-vole-ash

RBX1

None

58.84

False

7.2 kDa

63

MKMaksim Kuznetsov

id: soft-eagle-willow

Binder

LFM2-2.6B fine-tuned on peptide 3D structures

No preview available

--

--

--

--

--

58

MKMaksim Kuznetsov

id: deep-yak-leaf

Binder

LFM2-2.6B fine-tuned on peptide 3D structures

No preview available

--

--

--

--

--

67

MKMaksim Kuznetsov

id: rough-bear-topaz

Binder

LFM2-2.6B fine-tuned on peptide 3D structures

No preview available

--

--

--

--

--

56

MKMaksim Kuznetsov

id: vast-boar-willow

Binder

LFM2-2.6B fine-tuned on peptide 3D structures

No preview available

--

--

--

--

--

66

MKMaksim Kuznetsov

id: swift-swan-topaz

Binder

LFM2-2.6B fine-tuned on peptide 3D structures

No preview available

--

--

--

--

--

51

MKMaksim Kuznetsov

id: quick-moth-pine

Binder

LFM2-2.6B fine-tuned on peptide 3D structures

No preview available

--

--

--

--

--

65

MKMaksim Kuznetsov

id: swift-otter-iron

Binder

LFM2-2.6B fine-tuned on peptide 3D structures

No preview available

--

--

--

--

--

49

MKMaksim Kuznetsov

id: frozen-yak-vine

Binder

LFM2-2.6B fine-tuned on peptide 3D structures

No preview available

--

--

--

--

--

48

MKMaksim Kuznetsov

id: steady-bison-iron

Binder

LFM2-2.6B fine-tuned on peptide 3D structures

No preview available

--

--

--

--

--

59

MKMaksim Kuznetsov

id: hollow-moth-snow

Binder

LFM2-2.6B fine-tuned on peptide 3D structures

No preview available

--

--

--

--

--

66

MKMaksim Kuznetsov

id: noble-panther-opal

Binder

LFM2-2.6B fine-tuned on peptide 3D structures

No preview available

--

--

--

--

--

38

MKMaksim Kuznetsov

id: amber-cobra-birch

Binder

LFM2-2.6B fine-tuned on peptide 3D structures

No preview available

--

--

--

--

--

48

MKMaksim Kuznetsov

id: soft-lynx-flint

Binder

LFM2-2.6B fine-tuned on peptide 3D structures

No preview available

--

--

--

--

--

54

MKMaksim Kuznetsov

id: pale-eagle-willow

Binder

LFM2-2.6B fine-tuned on peptide 3D structures

No preview available

--

--

--

--

--

36

Rows per page

1-21 of 100