Appendix E — Model and Dataset Index

Model or Dataset	Main Use	Evidence Tier	Source
AlphaFold 2	Protein structure prediction	Demonstrated	Jumper et al., 2021
AlphaFold 3	Biomolecular interaction structure prediction	Demonstrated	Abramson et al., 2024
AlphaFold DB	Predicted protein structure database	Demonstrated	AlphaFold Protein Structure Database, 2026
ESMFold	Protein language model structure prediction	Demonstrated	Lin et al., 2023
ESM3	Multimodal protein language model	Demonstrated for selected generation tasks	Hayes et al., 2025
RFdiffusion	Protein backbone generation and design	Demonstrated	Watson et al., 2023
ProteinMPNN	Protein sequence design for structures	Demonstrated	Dauparas et al., 2022
Boltz-1	Open biomolecular interaction modeling	Demonstrated as an open research system	Boltz-1, 2024
Evo	Genome-scale biological sequence modeling	Demonstrated in published tasks	Nguyen et al., 2024
AlphaGenome	Regulatory variant-effect prediction	Demonstrated	Avsec et al., 2026
Geneformer	Single-cell gene and cell representations	Demonstrated	Theodoris et al., 2023
scGPT	Single-cell multi-omics foundation model	Demonstrated	Cui et al., 2024
GEARS	Genetic perturbation response prediction	Demonstrated in selected settings	Roohani et al., 2024
PDB	Experimental macromolecular structure archive	Demonstrated infrastructure	wwPDB, 2026
ChEMBL	Curated bioactivity database	Demonstrated infrastructure	Zdrazil et al., 2024
PubChem	Chemical substance, compound, and assay database	Demonstrated infrastructure	Kim et al., 2023
MoleculeNet	Molecular ML benchmark suite	Demonstrated benchmark	Wu et al., 2018
PoseBusters	Docking pose validity checks	Demonstrated benchmark	Buttenschoen et al., 2024