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Every biological foundation model, evaluated and ranked by the bio.rodeo team
Showing 49–72 of 1004 filtered models
Protein-protein interface prediction that summarizes molecular surface patches with persistent homology descriptors, at 0.77 test AUC.
Cryo-EM density enhancement for protein-ligand binding sites, sharpening weak ligand maps with a 3D Swin-Conv UNet trained on 6,511 complexes.
Peptide tandem mass spectrum prediction over a dictionary that pairs every canonical b and y fragment with its integer mass offsets.
Pan-allele peptide-MHC binding prediction unifying MHC class I and II, trained on a diversity-balanced set of 214 class I and 98 class II alleles.
Protein-ligand binding affinity scoring model for virtual screening that generalizes to novel pockets and ligands under strict train-test splits.
Hybrid diffusion-and-physics docking model that predicts protein-ligand binding poses and generalizes out-of-distribution for virtual screening.
Protein language model for microbial smORF-encoded small proteins, pairing multi-scale convolutions with transformer layers in a compact encoder.
Enzyme-substrate specificity prediction by end-to-end co-folding, with no predefined binding pocket. AUROC 0.766 on unseen enzymes and substrates.
Dual-target structure-based drug design that fuses two pocket-conditioned Bayesian flow distributions to generate 3D ligands binding both proteins.
Antibody-specific epitope prediction that replaces sequence-offset rotary attention with backbone local-frame 3D geometry. 0.410 MCC on AsEP.
Genome-scale synthetic lethality prediction for any human gene pair from Gene Ontology annotations, no protein interaction network required.
Signal peptide design framework that generates, filters, and ranks cargo-specific secretion signals using evolution-constrained discrete diffusion.
Structure-free virtual screening model co-embedding protein residues and small molecules from sequence and 2D chemistry, scoring a compound in 10 ms.
Lysine crotonylation site prediction for human non-histone proteins, fusing a frozen ProteinBERT feature branch with a sequence transformer.
Few-step generative model for de novo protein backbone design, extending MeanFlow to the SE(3) Lie-group geometry of residue frames.
Biosynthetic gene cluster discovery in plant genomes, transferring supervision from microbial BGCs by label-free adaptation over Pfam-domain tokens.
Preparation-free protein-ligand binding affinity prediction from a protein sequence and a ligand SMILES, using a cascaded mixture-of-experts fusion.
Residue-level prediction of ligand-binding and cryptic pockets in one model, reading frozen ESM-2 embeddings with no 3D structure at inference.
Protein complex structure prediction from amino acid sequence, deployed as a self-hosted SageMaker endpoint that returns mmCIF and ipTM confidence.
Cross-context protein binder design model that generates one sequence binding multiple targets or conformational states of the same target.
VHH nanobody expression predictor needing only an amino-acid sequence, no structure. Leave-program-out ROC-AUC 0.81 on unseen antibody programs.
Protein language model adding long-range contact supervision to ESM2 via LoRA, improving all eight protein-level tasks with no structural input.
Molecular glue degrader design model that jointly generates the glue molecule and the E3 ligase-target ternary complex from unbound monomers.