Every biological foundation model, evaluated and ranked by the bio.rodeo team
Showing 121–144 of 358 filtered models
Open-source Apache-2.0 reproduction of AlphaFold3 that predicts all-atom structures of proteins, RNA, DNA, small molecules, and their complexes.
Perturbation-trained single-cell foundation models (up to 3B parameters) that jointly model genes, cells, and compounds for precision oncology tasks.
Multimodal molecular large language model grounding molecule understanding and generation in fine-grained, multi-level chemical knowledge.
Structure prediction backbone that swaps AlphaFold3-style triangle attention for triangle multiplication, cutting compute without losing accuracy.
Molecular docking model that predicts protein-ligand binding poses with multi-stage Riemannian flow matching, yielding physically valid geometry.
Sequence-only interaction model scoring protein-protein and protein-ligand pairs plus functional annotation across whole proteomes in seconds.
De novo ligand design framework that generates protein binders and small molecules by inverting gradients through a differentiable docking model.
Graph diffusion transformer for in-context molecular design, adapting to new tasks from a few molecule-property demonstrations without fine-tuning.
SE(3)-equivariant flow-matching model for pocket-aware 3D ligand generation, predicting binding affinity and confidence in the same network.
Geometric deep learning scoring function for protein-ligand binding affinity, pretrained on synthetic complexes and fine-tuned on PDBbind structures.
Discrete flow generative model over fragmented SMILES for de novo, fragment-constrained, and property-optimized small-molecule drug design.
Sequence-based protein-ligand binding site predictor pairing a protein language model with a SMILES chemical language model for zero-shot ligands.
Multimodal drug-target interaction model aligning SMILES, molecule text, taxonomy, and protein sequence with a Gramian volume contrastive objective.
Spectroscopy-grounded molecular foundation model that reads NMR, IR, and mass spectra as text, elucidating structures and generating 3D conformers.
Structure-free RNA-small molecule binder discovery model that predicts ligands and their binding sites from RNA sequence using an RNA language model.
SE(3)-equivariant chemical language model for pocket-based 3D molecule generation, used to design an HPK1 inhibitor with in vivo anti-tumor efficacy.
Multimodal scientific foundation model unifying protein, DNA/RNA, and small-molecule structure in one token vocabulary for cross-domain reasoning.
Chemical language model for fragment-based drug discovery, trained on all 62M ZINC-22 fragments. Samples 99.9% chemically valid fragment SMILES.
Protein language model that predicts which of eight lipid categories a protein binds from sequence alone, plus binding sites and mutation effects.
Discrete graph diffusion model for multi-property molecular generation, composing per-property score guidance over arbitrary condition subsets.
Protein-ligand binding site prediction that ranks pocket residues and pocket center coordinates, staying accurate on AlphaFold-predicted structures.
Sequence-based multitask model predicting covalently ligandable cysteines and reversible ligand-binding residues across the human proteome.
RNA small-molecule binding site prediction from sequence alone, pairing frozen RiNALMo embeddings with a lightweight MLP classifier.