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Every biological foundation model, evaluated and ranked by the bio.rodeo team
Showing 73–96 of 218 filtered models
Mutation effect prediction at protein–DNA and protein–RNA interfaces, combining frozen ESM-2 embeddings with an edge-aware atomic graph network.
RNA interaction foundation model for conditional, zero-shot design of RNA sequences that bind protein, DNA, or RNA targets without retraining.
mRNA language model that tokenizes UTRs by nucleotide and coding regions by codon, aligned to protein sequence space through contrastive learning.
Conditional codon language model with 150M parameters that generates species-optimized coding sequences from a protein and its taxonomic lineage.
Open-source Apache-2.0 reproduction of AlphaFold3 that predicts all-atom structures of proteins, RNA, DNA, small molecules, and their complexes.
Efficient sequence-to-function transformer for regulatory genomics, matching Borzoi-class models while training in about a day on a single GPU.
Nucleic acid inverse-folding network that designs RNA sequences for a target 3D backbone and predicts protein-DNA binding specificity.
Multi-label classifier over ESM-2 embeddings that separates DNA-binding, RNA-binding, and dual-binding proteins using label-aware attention.
mRNA language model with a hyperbolic prediction head encoding the codon-amino-acid hierarchy, beating Euclidean baselines on 9 of 10 property tasks.
Cross-species RBP-RNA binding site predictor that turns RNA-binding protein conservation into label smoothing, reaching 0.85 AUC from human to mouse.
Structure-free RNA-small molecule binder discovery model that predicts ligands and their binding sites from RNA sequence using an RNA language model.
Isoform-resolved variant effect prediction from DNA sequence, using graph attention over transcript splice structures across 30 human tissues.
Splice donor and acceptor site prediction from raw DNA, scoring every position of a 20 kb window with an ensemble of dilated residual CNNs.
RNA secondary structure prediction that fuses base-pair priors from four orthogonal folding tools, reaching 0.709 F1 on cross-family bpRNA-new.
RNA small-molecule binding site prediction from sequence alone, pairing frozen RiNALMo embeddings with a lightweight MLP classifier.
RNA language model pretrained on 30M non-coding RNA sequences that predicts secondary structure, contacts, and splice sites without alignments.
RNA-small molecule binding affinity prediction from RNA sequence and compound SMILES, pairing a 56M-parameter RNA language model with ChemBERTa-2.
Codon language model trained with synonymous-codon-constrained masking, so its embeddings encode nucleotide-level signal, not amino acid identity.
RNA language model transfer-trained from ESM-2 via a pseudo-protein alphabet mapping, outperforming 12 RNA language models in zero-shot evaluation.
RNA foundation model pretrained jointly on sequences and secondary structures for structure prediction, homology and splice site classification.
Coaxial-stacking prediction for RNA multi-way junctions from sequence and secondary structure, at ~0.87 mean accuracy across 2- to 7-way topologies.
Splicing variant effect prediction across 49 human tissues and 15 developmental stages, from four weeks post conception to adulthood.