{"doi":"10.1038/s43588-024-00627-2","title":"MISATO: machine learning dataset of protein–ligand complexes for structure-based drug discovery","abstract":"Large language models have greatly enhanced our ability to understand biology and chemistry, yet robust methods for structure-based drug discovery, quantum chemistry and structural biology are still sparse. Precise biomolecule-ligand interaction datasets are urgently needed for large language models. To address this, we present MISATO, a dataset that combines quantum mechanical properties of small molecules and associated molecular dynamics simulations of ~20,000 experimental protein-ligand complexes with extensive validation of experimental data. Starting from the existing experimental structures, semi-empirical quantum mechanics was used to systematically refine these structures. A large collection of molecular dynamics traces of protein-ligand complexes in explicit water is included, accumulating over 170 μs. We give examples of machine learning (ML) baseline models proving an improvement of accuracy by employing our data. 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Popowicz","orcid":"0000-0003-2818-7498","position":12,"is_corresponding":false},{"id":3370,"name":"Erinç Merdivan","orcid":"0009-0004-9213-7393","position":13,"is_corresponding":false},{"id":53244,"name":"André Mourão","orcid":"0000-0003-0764-9868","position":14,"is_corresponding":false},{"id":53245,"name":"Píetro Lió","orcid":"0000-0002-0540-5053","position":15,"is_corresponding":false},{"id":3367,"name":"Till Siebenmorgen","orcid":"0009-0008-5160-8100","position":0,"is_corresponding":true}],"reference_count":78,"raw_metadata":null,"created_at":"2026-03-01T18:20:47.508186Z","pmid":"38730184","pmcid":"PMC11136668","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":"hybrid","license":"cc-by","views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":88.8889,"fair_a":75.0,"fair_i":20.0,"fair_r":41.6667,"fair_zscore":1.6051,"fair_rationale":{"fair_score":75.0,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":88.89,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"MISATO is publicly accessible and can be downloaded from Zenodo 77 ( https://zenodo.org/records/7711953 ).","grounded":true,"rationale":"The DOI 10.5281/zenodo.7711953 is a persistent identifier for the dataset. 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