To design binders for RBX1, I decided to use BoltzGen to design initial binder scaffolds, which would be later optimized by an ensemble of solMPNN and ThermoMPNN. For the BoltzGen binder scaffolds, I used the "protein-anything" design protocol with inverse folding, budgeting for the top 10 of 1,000 binder designs. These designs were then validated and filtered for ipTM > 0.7 by AlphaFold. Following filtering, I optimized the non-interfacing binder residues with the ProteinMPNN's soluble model, and orthogonally validated the resulting sequences with AlphaFold, taking the top-scoring MPNN sequence if it maintained an ipTM > 0.7. Finally, to optimize binder affinity and interfacing residues, I used ThermoMPNN and kept the top 5 most stabilizing (negative ddG) point-mutants.
id: vast-bear-frost
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id: steady-hawk-cloud
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id: azure-lion-dust
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id: ivory-shark-cypress
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id: calm-ant-ivy
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id: calm-lion-maple
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id: brisk-ibis-pine
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id: steady-quail-granite
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id: brisk-tiger-rose
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id: rough-lion-pine
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RBX1
0.69
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id: mellow-yak-plume
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id: golden-ram-lotus
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id: quick-lion-fern
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id: misty-swan-cloud
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id: scarlet-fox-wave
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id: lunar-lion-reed
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id: young-ram-clay
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id: dark-quail-cedar
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id: bright-panda-lotus
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id: violet-swan-granite
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id: silver-bat-sand
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