{ "meta": { "title": "The Legible Fold", "short": "AlphaFold", "runDate": "2026-07-27", "nextReview": "2026-10", "thesis": "AlphaFold made the whole protein universe legible, and it ships a per-residue confidence that tells you exactly where to trust it.", "generatedFrom": "AF-P04637-F1", "structureLicense": { "name": "CC-BY 4.0", "url": "https://creativecommons.org/licenses/by/4.0/", "holder": "AlphaFold Protein Structure Database (EMBL-EBI and Google DeepMind)" } }, "sources": { "jumper2021": { "id": "jumper2021", "title": "Highly accurate protein structure prediction with AlphaFold", "publisher": "Jumper et al., Nature", "year": "2021", "url": "https://www.nature.com/articles/s41586-021-03819-2" }, "casp14": { "id": "casp14", "title": "AlphaFold: a solution to a 50-year-old grand challenge in biology", "publisher": "Google DeepMind", "year": "2020", "url": "https://deepmind.google/discover/blog/alphafold-a-solution-to-a-50-year-old-grand-challenge-in-biology/" }, "anfinsen1973": { "id": "anfinsen1973", "title": "Principles that Govern the Folding of Protein Chains", "publisher": "Anfinsen, Science", "year": "1973", "url": "https://www.science.org/doi/10.1126/science.181.4096.223" }, "varadi2022": { "id": "varadi2022", "title": "AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space", "publisher": "Varadi et al., Nucleic Acids Research", "year": "2022", "url": "https://academic.oup.com/nar/article/50/D1/D439/6430488" }, "varadi2024": { "id": "varadi2024", "title": "AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences", "publisher": "Varadi et al., Nucleic Acids Research", "year": "2024", "url": "https://academic.oup.com/nar/article/52/D1/D368/7337620" }, "tunyasuvunakool2021": { "id": "tunyasuvunakool2021", "title": "Highly accurate protein structure prediction for the human proteome", "publisher": "Tunyasuvunakool et al., Nature", "year": "2021", "url": "https://www.nature.com/articles/s41586-021-03828-1" }, "abramson2024": { "id": "abramson2024", "title": "Accurate structure prediction of biomolecular interactions with AlphaFold 3", "publisher": "Abramson et al., Nature", "year": "2024", "url": "https://www.nature.com/articles/s41586-024-07487-w" }, "nobel2024": { "id": "nobel2024", "title": "The Nobel Prize in Chemistry 2024", "publisher": "The Royal Swedish Academy of Sciences", "year": "2024", "url": "https://www.nobelprize.org/prizes/chemistry/2024/summary/" }, "afdbEntry": { "id": "afdbEntry", "title": "AlphaFold DB entry: Cellular tumor antigen p53 (P04637)", "publisher": "AlphaFold Protein Structure Database, EMBL-EBI", "year": "2025", "url": "https://alphafold.ebi.ac.uk/entry/P04637" }, "afdbConfidence": { "id": "afdbConfidence", "title": "AlphaFold DB: confidence (pLDDT) and how to interpret it", "publisher": "AlphaFold Protein Structure Database, EMBL-EBI", "year": "2024", "url": "https://alphafold.ebi.ac.uk/faq" }, "pdb": { "id": "pdb", "title": "RCSB Protein Data Bank", "publisher": "RCSB PDB", "year": "2026", "url": "https://www.rcsb.org/" }, "uniprot": { "id": "uniprot", "title": "UniProtKB: Cellular tumor antigen p53 (P04637)", "publisher": "UniProt Consortium", "year": "2026", "url": "https://www.uniprot.org/uniprotkb/P04637/entry" } }, "casp": { "competition": "CASP14", "year": "2020", "medianGdt": { "value": 92.4, "src": "casp14" }, "backboneRmsdA": { "value": 0.96, "src": "jumper2021" }, "priorBestGdt": { "value": 60, "src": "casp14" }, "experimentalThresholdGdt": 90, "paper": "jumper2021" }, "database": { "atLaunchStructures": { "value": 1000000, "src": "varadi2022" }, "structures2024": { "value": 214000000, "src": "varadi2024" }, "pdbExperimentalStructures": { "value": 200000, "src": "pdb" }, "license": "CC-BY 4.0", "licenseUrl": "https://creativecommons.org/licenses/by/4.0/", "home": "https://alphafold.ebi.ac.uk/" }, "timeline": [ { "date": "1972", "title": "Anfinsen's dogma", "detail": "Christian Anfinsen's Nobel lecture crystallizes the premise: a protein's amino-acid sequence should determine its three-dimensional shape.", "src": "anfinsen1973" }, { "date": "2020", "title": "AlphaFold2 wins CASP14", "detail": "At the field's blind test, AlphaFold2 reaches a median GDT of 92.4, roughly experimental accuracy, on problems where prediction had stalled near 60 for years.", "src": "casp14" }, { "date": "2021", "title": "The method, and the human proteome, go public", "detail": "The Nature paper releases the method and code; a companion paper predicts nearly the entire human proteome and shows low confidence tracks intrinsic disorder.", "src": "jumper2021" }, { "date": "2022", "title": "The database opens the protein universe", "detail": "With EMBL-EBI, the AlphaFold Protein Structure Database expands from about a million predictions toward the whole cataloged protein universe, free and openly licensed.", "src": "varadi2022" }, { "date": "2024", "title": "AlphaFold 3 and a Nobel Prize", "detail": "AlphaFold 3 extends prediction from single chains to complexes with DNA, RNA, ions, and drug-like ligands; the Chemistry Nobel goes to Hassabis and Jumper for structure prediction and to Baker for protein design.", "src": "abramson2024" } ], "plddtBands": [ { "key": "veryHigh", "label": "Very high", "range": "pLDDT > 90", "min": 90, "meaning": "Backbone and side chains placed with near-experimental accuracy.", "src": "afdbConfidence" }, { "key": "confident", "label": "Confident", "range": "90 to 70", "min": 70, "meaning": "The general fold is right; expect small errors in the details.", "src": "afdbConfidence" }, { "key": "low", "label": "Low", "range": "70 to 50", "min": 50, "meaning": "Treat with caution. Often loops, linkers, and flexible edges.", "src": "afdbConfidence" }, { "key": "veryLow", "label": "Very low", "range": "pLDDT < 50", "min": 0, "meaning": "Very likely disordered: no single structure to place, not a failed one.", "src": "tunyasuvunakool2021" } ], "pipeline": [ { "key": "sequence", "title": "Sequence", "detail": "One protein: a string of amino acids, and nothing else to start from." }, { "key": "msa", "title": "Evolution", "detail": "Search millions of related sequences. Residues that mutate together across species tend to sit together in space." }, { "key": "evoformer", "title": "Evoformer", "detail": "Attention blocks pass information back and forth between the aligned sequences and every pair of residues." }, { "key": "structure", "title": "Structure", "detail": "Turn those abstract pairwise relationships into concrete 3D atomic coordinates." }, { "key": "confidence", "title": "Confidence", "detail": "Score every residue for how far to trust where it was placed. That score is pLDDT." } ], "demo": { "gene": "TP53", "name": "Cellular tumor antigen p53", "organism": "Homo sapiens", "uniprot": "P04637", "length": 393, "modelVersion": 6, "meanPlddt": { "value": 75.06, "src": "afdbEntry" }, "entry": "afdbEntry", "why": "p53 is a good teacher because it is half and half: a compact DNA-binding core that AlphaFold places with high confidence, flanked by tails it honestly marks as unplaceable.", "bandCounts": { "veryHigh": 206, "confident": 27, "low": 43, "veryLow": 117 }, "meanPlddtRederived": 75.06 }, "structure": { "meta": { "uniprot": "P04637", "uniprotId": "P53_HUMAN", "gene": "TP53", "name": "Cellular tumor antigen p53", "organism": "Homo sapiens", "taxId": 9606, "modelEntityId": "AF-P04637-F1", "modelVersion": 6, "modelCreatedDate": "2025-08-01", "pipeline": "AlphaFold Monomer v2.0 pipeline", "length": 393, "meanPlddt": 75.06, "bandFractions": { "veryHigh": 0.524, "confident": 0.069, "low": 0.109, "veryLow": 0.298 }, "boundingRadius": 65.5, 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