{"id":"doi:10.1093/nar/gkad1011","kind":"article","title":"AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences","authors":["Mihály Váradi","Damian Bertoni","Paulyna Magaña","Urmila Paramval","Ivanna Pidruchna","Malarvizhi Radhakrishnan","Maxim I. Tsenkov","Sreenath Sasidharan Nair","Milot Mirdita","Jingi Yeo","Oleg V. Kovalevskiy","Kathryn Tunyasuvunakool","Agata Laydon","Augustin Žídek","Hamish Tomlinson","Dhavanthi Hariharan","Josh Abrahamson","Tim Green","John Jumper","Ewan Birney","Martin Steinegger","Demis Hassabis","Sameer S Velankar"],"author_count":23,"year":2023,"published":"2023-10-18","venue":"Nucleic Acids Research","cited_by":2049,"doi":"10.1093/nar/gkad1011","arxiv_id":null,"nct_id":null,"source_url":"https://doi.org/10.1093/nar/gkad1011","archive_url":"https://space-kitty.com/papers/doi:10.1093/nar/gkad1011","updated":null,"pmid":"37933859","pmcid":"PMC10767828","openalex_id":"W4388464011","pdf_url":"https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkad1011/52777135/gkad1011.pdf","abstract":"The AlphaFold Database Protein Structure Database (AlphaFold DB, https://alphafold.ebi.ac.uk) has significantly impacted structural biology by amassing over 214 million predicted protein structures, expanding from the initial 300k structures released in 2021. Enabled by the groundbreaking AlphaFold2 artificial intelligence (AI) system, the predictions archived in AlphaFold DB have been integrated into primary data resources such as PDB, UniProt, Ensembl, InterPro and MobiDB. Our manuscript details subsequent enhancements in data archiving, covering successive releases encompassing model organisms, global health proteomes, Swiss-Prot integration, and a host of curated protein datasets. We detail the data access mechanisms of AlphaFold DB, from direct file access via FTP to advanced queries using Google Cloud Public Datasets and the programmatic access endpoints of the database. We also discuss the improvements and services added since its initial release, including enhancements to the Predicted Aligned Error viewer, customisation options for the 3D viewer, and improvements in the search engine of AlphaFold DB.","abstract_license":"CC-BY (publisher license, via OpenAlex)","license":"cc-by","is_open_access":true,"retracted":false,"peer_reviewed":null,"categories":["Protein Structure and Dynamics"],"details":null,"provenance":"openalex+europepmc","attribution":"Abstract of \"AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences\" by Mihály Váradi, Damian Bertoni, Paulyna Magaña et al., https://doi.org/10.1093/nar/gkad1011, used under its Creative Commons Attribution license (CC-BY); markup removed, otherwise unmodified.","topics":[{"slug":"protein-design","name":"AI Protein Design & Structure Prediction","domain_slug":"biotech"}],"cited_in_dossiers":[]}