Loading…
Every biological foundation model, evaluated and ranked by the bio.rodeo team
Showing 529–552 of 1102 filtered models
Codon optimization model for heterologous expression in E. coli, fine-tuning ProtBert to label each residue with an expression-weighted codon.
Antibody-antigen binding prediction from heavy chain, light chain, and antigen sequence, scoring 0.946 AUROC on a SARS-CoV-2 benchmark.
Long-context protein language model that reads whole viral genomes, using interaction-guided sparse attention over contexts of 61,000 amino acids.
De novo small-molecule generation inside a protein pocket, diffusing ligand atoms and pocket side chains together so the site adapts as it binds.
Protein conformation ensemble generation aligned to force-field energies, calibrating an AlphaFold 3-style diffusion model against MD thermodynamics.
Plant DNA-binding protein prediction that averages a ProtT5 sequence-embedding classifier with a SaProt structure-aware one at the score level.
Antibody caninisation model generating canine framework regions around given CDRs, released with a dataset of 430,000 canine antibody sequences.
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.
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.
Cyclic peptide design conditioned on target protein structure, generating all four cyclization types via all-atom, all-bond harmonic SDE modeling.
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.
Text-to-protein design retrieving natural protein fragments as a dynamic vocabulary, matching larger baselines on under 0.04% of their training data.
Protein-ligand binding affinity model that tokenizes quantum electron-cloud density into discrete codes, plus a distilled cloud-free variant.
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.
Protein structure prediction and peptide binder design model covering the 20 canonical amino acids plus 29 noncanonical residues.
RNA-binding protein predictor trained on eCLIP data that scores binding intensity along transcripts and recovers motifs via integrated gradients.