RATAN-PBind: ESM-2 embeddings and baseline models for de novo protein binder nomination

Large companion artefacts for RATAN-PBind (Retrieval-Augmented, Target-Aware Nomination for Protein Binding), a sequence-based pre-screen for de novo protein binders. Code and the headline model are at https://github.com/kartic03/RATAN-PBind. This record holds the files excluded from the repository for size: ESM-2 (esm2_t33_650M_UR50D) mean-pooled embeddings required to reproduce the prototype-similarity features, and the Random Forest, SVM, Extra Trees, and fine-tuned ESM-2 baseline models. This work used Proteinbase by Adaptyv Bio under the ODC-BY licence.