Biological models

59 model records in release 2026-09-22-f58a0f1d267f. Showing 1–24; page 1 of 3.

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

• Agro Nucleotide Transformer

  Genomics

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

• 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.

• Basenji

  Genomics

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

• 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.

• Chai-1

  Proteins and complexes · Molecular interactions

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

• ChromBPNet

  Genomics

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

• DiffDock-L

  Molecular interactions

  DiffDock-L places small-molecule ligands in protein structures using a diffusion docking model.

• DNABERT-2

  DNA and genomes

  DNABERT-2 learns DNA representations that can be adapted to genomic prediction tasks.

  Record: catalog-model-dnabert-2

• DNABERT-2

  Genomics

  DNABERT-2 learns DNA representations that can be adapted to genomic prediction tasks.

  Record: discovery-model-dnabert-2

• DreaMS

  Metabolomics

  DreaMS learns molecular representations from tandem mass spectra using self-supervised learning.

• ESM-1v

  Protein function

  ESM-1v provides protein language models intended for zero-shot variant-effect scoring.

• ESM-2

  Proteins and complexes

  ESM-2 is a family of protein sequence encoders that produce representations for downstream protein analyses.

  Record: catalog-model-esm-2

• ESM-2

  Protein function

  ESM-2 is a family of protein sequence encoders that produce representations for downstream protein analyses.

  Record: discovery-model-esm-2

• ESM-IF1

  Protein structure

  ESM-IF1 designs protein sequences conditioned on backbone coordinates.

• ESM3

  Protein structure

  ESM3 generates and completes protein sequence, structure and functional annotations using a shared multimodal representation.

• ESMC

  Protein function

  ESM C learns protein sequence representations for downstream analysis.

• ESMFold

  Proteins and complexes

  ESMFold predicts protein structures directly from amino-acid sequence using ESM-2 representations.

  Record: catalog-model-esmfold

• ESMFold

  Protein structure

  ESMFold predicts protein structures directly from amino-acid sequence using ESM-2 representations.

  Record: discovery-model-esmfold

• ESMFold2

  Protein structure

  ESMFold2 predicts biomolecular structures from protein, DNA, RNA and ligand inputs, optionally using protein alignments.

• Evo 2

  DNA and genomes · Microbes and communities

  Evo 2 models and generates DNA over long contexts at single-nucleotide resolution.

  Record: catalog-model-evo-2

• Evo 2

  Genomics

  Evo 2 models and generates DNA over long contexts at single-nucleotide resolution.

  Record: discovery-model-evo-2

• GEARS

  Cells and tissues

  GEARS predicts transcriptional responses to single- and multi-gene perturbations from single-cell perturbation screens.

  Record: catalog-model-gears

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.