Biological models

240 model records in release 2026-10-12-fcce59cc481b (gzip). Showing 1–24; page 1 of 10.

Evaluated configurations, methods and pipelines are listed separately. Names alone do not establish equivalent models or checkpoints.

• Agro Nucleotide Transformer

  DNA and genomes

  AgroNT learns DNA representations from plant reference genomes for plant molecular prediction tasks.

• AIDO Protein-RAG

  Proteins and complexes

  Retrieval-augmented protein language model from the AIDO.Protein-RAG work, which combines a pretrained protein language model with retrieved multiple sequence alignments; ProteinGym lists AIDO with alignment and structure inputs and scores it as a zero-shot substitution baseline.

• AIDO.DNA

  DNA and genomes

  AIDO.DNA genomic language model.

• AIDO.RNA

  Microbes and communities · DNA and genomes

  AIDO.RNA RNA language model family.

• Akita

  DNA and genomes

  Akita contact-map model.

• AlphaFold 2

  Protein structure · Proteins and complexes

  Deep-learning protein structure prediction model evaluated in this comparison.

• AlphaFold 3

  Protein structure

  AlphaFold 3 predicts three-dimensional structures of complexes containing proteins, nucleic acids and other molecular components. It combines a Pairformer representation network with an atomic-coordinate diffusion model. This entry describes the model and local implementation; the hosted AlphaFold Server has a separate profile.

• AlphaGenome

  DNA and genomes

  AlphaGenome predicts regulatory activity and variant effects from long DNA sequences, with outputs for expression, splicing, chromatin and contact maps.

• AttentiveFP

  Protein function

  Attentive fingerprint graph network.

• Basenji

  DNA and genomes

  Basenji predicts quantitative regulatory activity along DNA and scores the effects of sequence changes.

• BioFM

  DNA and genomes

  BioFM genomic foundation model family as listed on the GENEB leaderboard.

• BiRNA-BERT

  Microbes and communities · DNA and genomes

  BiRNA-BERT RNA language model.

• Boltz

  Molecular interactions

  Boltz predicts biomolecular complex structures; Boltz-2 also predicts binding affinity.

• Boltz-2

  Molecular interactions

  Boltz predicts biomolecular complex structures; Boltz-2 also predicts binding affinity.

• Borzoi

  DNA and genomes

  Model trained to predict RNA-seq coverage from DNA sequence.

• BPNet

  DNA and genomes

  BPNet convolutional architecture trained from scratch per task.

• Caduceus

  DNA and genomes

  Self-supervised DNA language model pretrained on human genomic sequence.

• CARP

  Proteins and complexes

  Convolutional protein language model pretrained by masked language modelling on protein sequences, scored in ProteinGym as a zero-shot single-sequence substitution baseline.

• CellPLM

  Single cell · Spatial omics

  Cell-level transformer foundation model pretrained on scRNA-seq and spatial transcriptomics (Wen et al., ICLR 2024).

• Chai-1

  Proteins and complexes · Molecular interactions

  Chai-1 predicts the structures of biomolecular complexes containing proteins, nucleic acids and small molecules.

• ChemLLM-7B

  Protein function

  ChemLLM-7B chemistry large language model, prompted for protein property questions.

• Chroma

  Protein structure

  Diffusion-based protein backbone generation method evaluated in Scaffold-Lab (released 2023-11).

• ChromBPNet

  DNA and genomes

  ChromBPNet predicts base-resolution chromatin accessibility while modeling assay-specific enzyme bias separately.

• CI-SpliceAI

  DNA and genomes

  SpliceAI reimplementation retrained on a collapsed isoform set of manually curated GENCODE HAVANA splice sites from all chromosomes.

This index reflects a dated catalogue, not an exhaustive census. Source checking does not mean independent reproduction; compare results only under compatible protocols, datasets and metrics.