The design method in uses BAGEL, leveraging protein language model embeddings (e.g., ESM-2) of interface residues to identify new binder sequences whose embedding profiles resemble those of known complexes. Candidate sequences are clustered, folded, and filtered using MMseqs2, Boltz-2, and structural metrics such as pLDDT, iPAE, and ipSAE to select the most promising designs.
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