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Every biological foundation model, evaluated and ranked by the bio.rodeo team
Showing 913–936 of 1004 filtered models
Structure-aware antibody language model with sequence embeddings contrastively aligned to crystal structures, reaching AUROC 0.875 on HER2 binding.
Antibody language model pretrained on 779M human B cell receptor sequences, reading a heavy chain, a light chain, or both paired in one input.
Zero-shot variant effect prediction that fuses a frozen protein language model with an equivariant graph network over residue contact graphs.
AlphaFold fine-tuned via OpenFold on 944 high-resolution MHC-peptide structures, reaching median peptide RMSD of 0.65 Å on held-out complexes.
Protein structure tokenizer that encodes all-atom folds as artificial amino acids and decodes them back to coordinates at TM-score above 0.96.
Sequence-only cancer driver mutation predictor combining ProtT5-XL embeddings with per-position evolutionary statistics and a confidence score.
Full-precision LoRA fine-tuning of ESM-2 for per-residue binding site prediction, where low-rank constraints curb overfitting on small datasets.
4-bit QLoRA fine-tunes of ESM-2 for per-residue protein binding site prediction, released as a checkpoint family spanning 8M to 650M parameters.
Diffusion model for programmable protein design that jointly samples structures and sequences, conditioned on symmetry, shape, or text prompts.
Protein motif-scaffolding driven by a protein language model instead of MSA pretraining, solving 22 of 24 benchmark problems with diverse backbones.
Protein language models from 151M to 6.4B parameters, trained on over a billion sequences for sequence generation and zero-shot fitness prediction.
Encoder-decoder framework unifying molecules, proteins, and natural language with SELFIES notation for cross-modal drug discovery tasks.
Conditional GAN that generates small molecules against a protein-protein interaction interface, encoding the complex with graph attention networks.
MSA-free protein structure prediction that replaces multiple sequence alignments with a protein language model pre-trained on billions of sequences.
De novo protein backbone generation by SE(3) flow matching, with motif-scaffolding built in. Samples a designable backbone in seconds on one GPU.
Structure-aware protein language model pairing amino acid tokens with Foldseek 3Di structural states, outperforming ESM-2 across 10 downstream tasks.
Interface residue accuracy estimation for protein complexes, predicting per-residue lDDT from whole-complex, per-monomer and cross-chain features.
Missense variant pathogenicity predictor built on AlphaFold 2 representations, scoring variants across the human proteome at 0.940 AuROC on ClinVar.
Codon-vocabulary protein language model that converts ProtBERT to 64 codon tokens via embedding seeding, masked pretraining, and distillation.
Discrete diffusion model for protein sequence and MSA generation, enabling controllable de novo design directly in sequence space without structure.
Antibody CDR design framework pairing a pretrained antibody language model with a hierarchical graph neural network for one-shot CDR generation.
Protein language model ranking stabilizing mutations with no assay data, trained jointly to predict the growth temperature of each sequence's host.