All Competitors
Every biological foundation model, evaluated and ranked by the bio.rodeo team
Showing 25–48 of 90 filtered models
MMPT-FM
389—Chemical language model that generates matched molecular pair transformations from SMILES and SMARTS to design medicinal-chemistry analogs.
Small moleculeLanguage model82OpennessPeptideCLM-2
101—Chemical language models pretrained on SMILES for therapeutic peptides, natively representing non-canonical residues, cyclization, and conjugation.
Small moleculeProtein79OpennessLinkLlama
10113Molecular linker design model fine-tuned from Llama 3 that emits PROTAC and fragment linkers as SMILES from natural-language geometry prompts.
Small molecule27OpennessEnzyGen2
30——Protein foundation model for de novo enzyme design that co-designs sequence and 3D structure under small-molecule ligand guidance, at 730M parameters.
ProteinSmall molecule89OpennessSuiren-1.0
174—Molecular foundation models pretrained on density functional theory data, encoding 3D geometry and quantum behavior for ADMET and drug discovery.
Small molecule46OpennessSELFormerMM
358—Multimodal molecular foundation model fusing SELFIES, 2D graphs, text, and knowledge graphs via contrastive pretraining for property prediction.
Small molecule55OpennessHorizyn-1
12203—Dual-encoder contrastive model that retrieves enzymes for query reactions by matching reaction fingerprints to protein sequence embeddings.
ProteinSmall molecule21OpennessATOMICA
—3—Geometric deep learning model that learns atomic-scale representations of molecular interfaces across proteins, small molecules, and nucleic acids.
ProteinSmall moleculeRNA88OpennessAnewOmni
842—All-atom generative foundation model that designs small molecules, peptides, and nanobodies against a target binding site from a single checkpoint.
ProteinSmall molecule63OpennessAetherCell
192—Generative virtual-cell model predicting whole-transcriptome responses to unseen compounds and genetic perturbations, from cell lines to organoids.
Single-cellSmall molecule29OpennessMolecular 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 model7OpennessMultiPUFFIN
—978—Multimodal foundation model pretrained on ~500K unlabeled PubChem molecules that jointly predicts nine thermophysical properties of small molecules.
Small molecule10OpennessMAP
—71—Shanghai Jiao Tong UniversityFebruary 25, 2026contrastive_learningdrug_response_predictiongraph_neural_network+6Knowledge-graph-grounded model that predicts single-cell transcriptomic responses to small molecules, with zero-shot prediction for unprofiled drugs.
Single-cellSmall molecule12OpennessCellAwareGNN
—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
—4—Polarizable machine-learning interatomic potential extending MACE with long-range electrostatics, trained on 100M OMol25 DFT calculations.
Small moleculeProtein19OpennessMMPT-RAG
—1—Retrieval-augmented model for matched molecular pair transformations, proposing localized analog edits guided by retrieved reference compounds.
Small molecule16OpennessMolDeBERTa
45906SMILES molecular encoder on a DeBERTaV2 backbone, pretrained on 123M PubChem molecules with physicochemical and structural-similarity objectives.
Small molecule25OpennessBioKinema
—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 molecule13OpennessUBio-MolFM
33—7Universal all-atom machine-learning force field for molecular dynamics, with ab initio-level accuracy on solvated biomolecules of ~1,500 atoms.
Small moleculeProtein81OpennessTerraBind
—55—Protein-ligand foundation model that maps coarse-grained structural representations directly to binding affinity, running ~26x faster than Boltz-2.
ProteinSmall molecule24OpennessBioLM-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 molecule8OpennessAtomPaint
———Full-atom SE(3)-equivariant diffusion model that inpaints binding interfaces to design proteins that bind DNA, RNA, and small molecules.
ProteinSmall molecule19Openness