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Every biological foundation model, evaluated and ranked by the bio.rodeo team
Showing 409–432 of 1004 filtered models
Structure-based drug design model that inpaints a 3D ligand density into an empty protein pocket, then decodes those voxels into valid SMILES.
Nanomaterial-protein interaction prediction from protein sequence, structure, and experimental context that generalizes to unseen materials.
Structure-based drug design model that generates 3D ligands inside a protein pocket by interpolating distribution parameters instead of samples.
Antibody inverse folding by discrete diffusion, sampling sequences that fold onto a given backbone. Generates varied CDRs at high sequence recovery.
Scoring function for protein, nucleic acid, and small-molecule complexes that predicts binding affinity, ranks docked poses, and screens ligands.
Plant immune receptor-ligand classifier that scores MAMP epitope immunogenicity from sequence, reaching 73% accuracy on a held-out test set.
Enzyme Commission number prediction that pools ESM Cambrian embeddings across unlabeled sequence homologs, scoring 0.788 F1 on full 4-digit EC.
Protein multi-conformation predictor that scores per-residue flexibility, then masks MSA columns to steer AlphaFold 2 toward alternative states.
Conditional chemical language model prompted with a protein target and mechanism of action to score and design molecules without structural input.
Protein-DNA binding free energy change prediction for missense mutations, with double- and single-stranded DNA binders modeled separately.
Protein foundation model built on Bayesian Flow Networks, prompted with MSA profiles for structure- and function-preserving sequence design.
Fungal genome mining framework that detects biosynthetic gene clusters and identifies their core enzymes from a pretrained Pfam-domain transformer.
Antibody, nanobody, and T-cell receptor structure prediction that resolves bound and unbound conformations separately in under a second per domain.
Site-specific structure prediction conditioning AlphaFold3 diffusion on a fixed receptor and known binding pocket. 81.2% success on PoseBusters V2.
Antimicrobial discovery model predicting compound potency against unseen bacterial strains and generating de novo antibiotics from pathogen genomes.
De novo design of heavy metal-binding peptides by classifier-guided diffusion over ESM-2 embeddings, with Cu and Zn binders validated in vitro.
Spatial proteomics imputation model inferring surface protein abundance from transcriptomics-only tissue sections via dual graph attention networks.
Structure-based 3D molecule generation with one diffusion backbone for fragment growing, linker design, scaffold hopping, and side-chain decoration.
Peptide toxicity classification that fuses ESM-2 embeddings with an ESMFold-predicted residue contact graph read by a graph transformer.
Mutational effect predictor for protein-protein binding energy, matching the FoldX force field's accuracy with a 1,000x speed-up.
De novo protein backbone generator trained on low-confidence AlphaFold structures as corrupted data, reaching 86% designability at 700 residues.
Single-sequence protein structure predictor that adapts image diffusion to generate 2D inter-residue templates, folding proteins without an MSA.
Gradient-free protein design framework that treats engineering as Monte Carlo sampling of a user-defined energy landscape over pretrained models.
De novo protein binder design that conditions AlphaFold2-Multimer hallucination on a chosen fold, from TIM barrels to VHH nanobody scaffolds.