All Competitors
Every biological foundation model, evaluated and ranked by the bio.rodeo team
Showing 121–144 of 217 filtered models
EDEN
—4—Metagenomic foundation model trained on 9.7 trillion nucleotide tokens for generative therapeutic design across genes, peptides, and microbiomes.
DNA & GeneProtein13OpennessAAVDiffusion
—2—Diffusion model for de novo AAV capsid design that steers sampling with a viability classifier toward assemblable, packaging-competent variants.
Protein5OpennessSingle-cell RNA-seq language model that treats cells as gene-expression tokens, synthesizing whole transcriptomes from tissue and disease metadata.
Single-cellSpatial omics2OpennessSequence-only latent diffusion model that designs target-specific peptide binders, cascaded with an affinity classifier through joint optimization.
ProteinSmall molecule4OpennessSurfFlow
—6—Flow-matching model for therapeutic peptide design that co-designs sequence, structure, and molecular surface to disrupt protein-protein interactions.
ProteinSmall molecule18OpennessGEMGen
—2—Generative language model for phenotype-driven drug discovery, proposing small-molecule structures from up- and down-regulated gene signatures.
Small moleculeSingle-cell9OpennessGenoME
—1—Mixture-of-Experts generative model turning DNA sequence plus cell-type ATAC-seq into unified epigenomic, transcriptomic, and 3D chromatin profiles.
DNA & GeneSingle-cell8OpennessmRNA-GPT
41—GPT-style generative language model for mRNA coding sequences, pretrained across bacteria, eukaryotes, and archaea for de novo CDS design.
RNA39OpennessFOCUS
———Generative foundation model that imputes genes and denoises spatial transcriptomics, conditioned on H&E histology, scRNA-seq, and spatial priors.
Spatial omicsPathologySingle-cell4OpennessNucleotide Transformer v3 (NTv3)
901234.8KMulti-species genomics foundation model spanning representation learning, functional-track prediction, and sequence generation at 1 Mb context.
DNA & Gene25OpennessProFam
582—Protein-family language model trained on unaligned homolog sets for zero-shot variant fitness prediction and design. ProFam-1 holds 251M parameters.
Protein86OpennessPXDesign
23825—De novo protein binder design suite from ByteDance pairing diffusion and hallucination generators with confidence-based filtering of designs.
Protein65OpennessHD-Prot
74—Multimodal protein language model that adds a continuous-token diffusion head to a discrete pLM, modeling structure without vector quantization.
Protein14OpennessSynPROTAC
———Designs synthesizable PROTAC degraders from reaction templates and purchasable building blocks, with reinforcement learning tuning the generator.
Small molecule11OpennessProteinEBM
—7—Energy-based model of protein conformational space, turning a diffusion model into a statistical potential for structure ranking and mutation scoring.
Protein8OpennessOMTRA
68——Structure-based drug design model that unifies de novo generation, docking, conformer generation, and pharmacophore conditioning via flow matching.
Small moleculeProtein72OpennessTriFlow
9——Structure-conditioned protein sequence design, pairing a three-track architecture with discrete flow matching for fast, few-step inverse folding.
Protein69OpennessgRNAde
310321MRC Laboratory of Molecular Biology +1 otherDecember 1, 2025de_novo_designgenerativegraph_neural_network+5RNA inverse-folding model that generates sequences predicted to fold into a target 3D backbone, capturing non-canonical pairs and tertiary motifs.
RNA98OpennessRadDiff
———Retrieval-augmented diffusion model for protein inverse folding that conditions sequence generation on profiles from structurally similar homologs.
Protein27OpennessSpatial transcriptomics language model that reads tissue as spatial sentences to simulate cell profiles and run in silico perturbations.
Spatial omicsSingle-cell53Openness- University of Maryland, College ParkNovember 24, 2025codon_optimizationde_novo_designfoundation_model+6
Conditional codon language model with 150M parameters that generates species-optimized coding sequences from a protein and its taxonomic lineage.
DNA & GeneRNA90Openness Micellangelo
———Eindhoven University of TechnologyNovember 24, 2025cell_biologycell_morphology_simulationconditional_generation+5Flow-matching generative model that synthesizes fluorescence images of human fibroblasts conditioned on surface micro-topographies.
Imaging5OpennessMIMYR
—2—Generative framework that reconstructs missing spatial transcriptomics regions by jointly predicting cell locations, cell types, and gene expression.
Spatial omicsSingle-cell16Openness