We employ BAGEL (https://github.com/softnanolab/bagel, https://www.biorxiv.org/content/10.1101/2025.07.05.663138v2) with a protein language model (ESM-2) and sample binder variants from the receptor bound complex (PDB ID: 2VSM). More specifically, we find binder sequences that lead to a very similar embedding direction in the interface in the target viral protein. We do this by using an EmbeddingsSimilarityEnergy in BAGEL, penalizing deviation of such embeddings compared in the receptor-bound complex, to the complex with our newly perturbed/designed sequence.
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