All Competitors
Every biological foundation model, evaluated and ranked by the bio.rodeo team
Showing 25–48 of 79 filtered models
SELFormerMM
3——Multimodal molecular foundation model fusing SELFIES, 2D graphs, text, and knowledge graphs via contrastive pretraining for property prediction.
Small molecule55OpennessAnewOmni
842—All-atom generative foundation model that designs small molecules, peptides, and nanobodies against a target binding site from a single checkpoint.
ProteinSmall molecule63OpennessMolecular reasoning model built on DeepSeek-7B, using chain-of-thought and reinforcement learning for property prediction, generation, and reactions.
Small moleculeLanguage model21OpennessSmall-molecule drug discovery foundation model covering ADMET, retrosynthesis, drug-target activity, and molecular optimization in a 2.6B checkpoint.
Small moleculeLanguage model7OpennessMolX
—1—Monash UniversityMarch 1, 2026antibody_drug_conjugate_designbinding_affinity_predictiondrug_discovery+10Graph-transformer foundation model pretrained on 3M protein pockets and 5M molecules as E(3)-equivariant graphs for protein-ligand representation.
Protein11OpennessMultiPUFFIN
———Multimodal foundation model pretrained on ~500K unlabeled PubChem molecules that jointly predicts nine thermophysical properties of small molecules.
Small molecule10OpennessLarge language model trained on functional genomics data to prioritize novel therapeutic targets from genome-wide CRISPR knockout screens.
DNA & GeneLanguage model12OpennessCellAwareGNN
—1—Vanderbilt University Medical CenterFebruary 23, 2026drug_discoveryfoundation_modelgraph_neural_network+4Knowledge-graph foundation model for drug repurposing, grounding a biomedical graph in cell-type-specific genetic associations to rank indications.
Single-cellSmall molecule11OpennessMACE-POLAR-1
—16—Polarizable machine-learning interatomic potential extending MACE with long-range electrostatics, trained on 100M OMol25 DFT calculations.
Small moleculeProtein19OpennessMMPT-RAG
———Retrieval-augmented model for matched molecular pair transformations, proposing localized analog edits guided by retrieved reference compounds.
Small molecule16OpennessBioKinema
—3—International Digital Economy AcademyFebruary 15, 2026conformational_samplingdiffusiondrug_discovery+5Diffusion model that generates continuous-time, all-atom biomolecular trajectories, reproducing conformational kinetics far more cheaply than MD.
ProteinSmall molecule13OpennessTerraBind
———Protein-ligand foundation model that maps coarse-grained structural representations directly to binding affinity, running ~26x faster than Boltz-2.
ProteinSmall molecule24OpennessIsoDDE
———Unified drug design engine for protein-ligand structure prediction, binding affinity estimation, and compound generation from Isomorphic Labs.
Protein13OpennessBioLM-Score
———Shenzhen UniversityFebruary 9, 2026binding_affinity_predictiondrug_discoverymixture_density_network+4Protein-ligand scoring function that conditions probabilistic geometric potentials on language model priors to rank docked poses and binding affinity.
ProteinSmall molecule11OpennessE(3)-equivariant diffusion model for macrocycle design that turns acyclic molecules into macrocycles, with a transformer choosing where to cyclize.
Small molecule8OpennessFoldVision
———Structure-based protein encoder that voxelizes every heavy atom into a 3D grid, learning orientation-robust representations for protein function.
Protein20OpennessAQAffinity
—16—Structure-free protein-ligand binding affinity predictor built on OpenFold3 that scores potency from a protein sequence and a ligand SMILES string.
ProteinSmall molecule64OpennessConGLUDe
———Johannes Kepler University LinzJanuary 14, 2026binding_site_predictioncontrastive_learningdrug_discovery+7Contrastive geometric model unifying structure- and ligand-based drug design for zero-shot virtual screening, target fishing, and pocket selection.
ProteinSmall molecule8OpennessNetMedGPT
—2—Transformer foundation model pretrained on a biomedical knowledge graph for zero-shot drug repurposing, target, and adverse-effect prediction.
Language modelSmall molecule24OpennessGEMGen
—2—Generative language model for phenotype-driven drug discovery, proposing small-molecule structures from up- and down-regulated gene signatures.
Small moleculeSingle-cell9OpennessPeptiVerse
———University of Pennsylvania +1 otherJanuary 3, 2026binding_affinity_predictiondrug_discoverygradient_boosting+4Peptide developability predictor scoring solubility, permeability, toxicity, and binding from amino-acid sequences or chemically modified SMILES.
ProteinSmall molecule81OpennessSynPROTAC
———Designs synthesizable PROTAC degraders from reaction templates and purchasable building blocks, with reinforcement learning tuning the generator.
Small molecule11OpennessOMTRA
68——Structure-based drug design model that unifies de novo generation, docking, conformer generation, and pharmacophore conditioning via flow matching.
Small moleculeProtein72OpennessFlexiFlow
—1—Flow-matching model that jointly samples 3D de novo molecules and several low-energy conformers, extending to pocket-conditioned ligand design.
Small moleculeProtein19Openness