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Every biological foundation model, evaluated and ranked by the bio.rodeo team
Long-context protein language model that reads whole viral genomes, using interaction-guided sparse attention over contexts of 61,000 amino acids.
Protein conformation ensemble generation aligned to force-field energies, calibrating an AlphaFold 3-style diffusion model against MD thermodynamics.
Antibody caninisation model generating canine framework regions around given CDRs, released with a dataset of 430,000 canine antibody sequences.
Plant DNA-binding protein prediction that averages a ProtT5 sequence-embedding classifier with a SaProt structure-aware one at the score level.
Protein-ligand docking model for high-throughput virtual screening, predicting binding poses with graph neural networks at low computational cost.
Diffusion protein language model for de novo design conditioned jointly on GO terms, InterPro domains, EC numbers, motifs, and backbone structure.
Missense variant effect predictor that scores mutations from Δ-embeddings — wild-type minus mutant protein language model representations.
Intrinsically disordered region function prediction, scoring every residue for five binding subtypes plus disordered flexible linkers.
Cyclic peptide design conditioned on target protein structure, generating all four cyclization types via all-atom, all-bond harmonic SDE modeling.
Linear B-cell epitope prediction for cancer antigens, pairing ESM-2 embeddings with an MLP classifier; ROC-AUC 0.94 on a held-out IEDB benchmark.
De novo protein binder design that recasts structure-predictor confidence as an energy function, replacing ipTM as the hallucination objective.
Protein structure retrieval model aligning 3D structures with functional text via contrastive learning, for zero-shot search of PDB and cryo-EM maps.
Protein-ligand binding affinity model that tokenizes quantum electron-cloud density into discrete codes, plus a distilled cloud-free variant.
Text-to-protein design retrieving natural protein fragments as a dynamic vocabulary, matching larger baselines on under 0.04% of their training data.
Sequence-only predictor of protein stability change on point mutation, scoring both ddG and melting temperature shift without any input structure.
Protein conformation and dynamics generation from MD data, sampling trajectories, independent ensembles, and interpolations between two known states.
RNA-binding protein predictor trained on eCLIP data that scores binding intensity along transcripts and recovers motifs via integrated gradients.
Protein structure prediction and peptide binder design model covering the 20 canonical amino acids plus 29 noncanonical residues.
Molecular dynamics emulator generating time-coarsened trajectories for small molecules, peptides, and proteins from one shared atomic representation.
Protein-DNA binding prediction and binder design from sequence, aligning protein and DNA language model embeddings instead of co-folding a complex.