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Linear antibody epitope prediction using AlphaFold2.

Λεπτομέρειες βιβλιογραφικής εγγραφής
Τίτλος: Linear antibody epitope prediction using AlphaFold2.
Συγγραφείς: DeRoo J; School of Biomedical Engineering, Colorado State University, Fort Collins, United States., Terry JS; Department of Microbiology, Immunology, & Pathology, Colorado State University, Fort Collins, United States., Zhao N; Department of Biochemistry and Molecular Genetics, University of Colorado-Anschutz Medical Campus, Aurora, United States., Stasevich TJ; Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States., Snow C; School of Biomedical Engineering, Colorado State University, Fort Collins, United States.; Department of Chemical & Biological Engineering, Colorado State University, Fort Collins, United States., Geiss BJ; School of Biomedical Engineering, Colorado State University, Fort Collins, United States.; Department of Microbiology, Immunology, & Pathology, Colorado State University, Fort Collins, United States.
Πηγή: ELife [Elife] 2026 Sep 18; Vol. 13. Date of Electronic Publication: 2026 Sep 18.
Τύπος έκδοσης: Journal Article
Γλώσσα: English
Στοιχεία περιοδικού: Publisher: eLife Sciences Publications, Ltd Country of Publication: England NLM ID: 101579614 Publication Model: Electronic Cited Medium: Internet ISSN: 2050-084X (Electronic) Linking ISSN: 2050084X NLM ISO Abbreviation: Elife Subsets: MEDLINE
Imprint Name(s): Original Publication: Cambridge, UK : eLife Sciences Publications, Ltd., 2012-
Ιατρικοί όροι (MeSH): Epitopes*/immunology , Epitopes*/chemistry , Epitope Mapping*/methods , Computational Biology*/methods, Antibodies, Monoclonal/immunology ; Antibodies, Monoclonal/chemistry ; Prediction Algorithms ; Algorithms ; Humans
Περίληψη: Defining the binding epitopes of antibodies is essential for understanding how they bind to their antigens and perform their molecular functions. However, while determining linear epitopes of monoclonal antibodies can be accomplished utilizing well-established empirical procedures, these approaches are generally labor- and time-intensive, and costly. To take advantage of the recent advances in protein structure prediction algorithms available to the scientific community, we developed a calculation pipeline based on the localColabFold implementation of AlphaFold2 that can predict linear antibody epitopes by predicting the structure of the complex between antibody heavy and light chains and target peptide sequences derived from antigens. We found that this AlphaFold2 pipeline, which we call PAbFold, was able to accurately flag known epitope sequences for several well-known antibody targets (HA/Myc) when the target sequence was broken into small overlapping linear peptides and antibody complementarity determining regions were grafted onto several different antibody framework regions in the single-chain antibody fragment format. To determine if this pipeline was able to identify the epitope of a novel antibody with no structural information publicly available, we determined the epitope of a novel anti-SARS-CoV-2 nucleocapsid-targeted antibody using our method and then experimentally validated our computational results using peptide competition ELISA assays. These results indicate that the AlphaFold2-based PAbFold pipeline we developed is capable of accurately identifying linear antibody epitopes in a short time using just antibody and target protein sequences. This emergent capability of the method is sensitive to methodological details such as peptide length, AlphaFold2 neural network versions, and multiple-sequence alignment databases. PAbFold is available at https://github.com/jbderoo/PAbFold.
(© 2024, DeRoo et al.)
Competing Interests: JD, JT, NZ, CS, BG No competing interests declared, TS Reviewing editor, eLife
Σχόλια: Update of: bioRxiv. 2024 Dec 20:2024.04.19.590298. doi: 10.1101/2024.04.19.590298.. (PMID: 38659833)
References: Nat Commun. 2023 Apr 25;14(1):2389. (PMID: 37185622)
Nucleic Acids Res. 2000 Jan 1;28(1):214-8. (PMID: 10592229)
Biophys J. 1998 Jul;75(1):422-7. (PMID: 9649402)
Nat Protoc. 2023 Jun;18(6):1814-1840. (PMID: 37188806)
J Res Natl Inst Stand Technol. 2019 Oct 09;124:1-6. (PMID: 34877177)
Proteins. 2023 Feb;91(2):171-182. (PMID: 36088633)
Nat Commun. 2024 Aug 10;15(1):6867. (PMID: 39127753)
Front Immunol. 2022 Sep 15;13:960985. (PMID: 36189325)
Structure. 2020 Jan 7;28(1):119-129.e2. (PMID: 31727476)
Curr Opin Struct Biol. 2022 Jun;74:102379. (PMID: 35490649)
Commun Biol. 2023 May 29;6(1):575. (PMID: 37248282)
J Mol Biol. 2016 Oct 9;428(20):3885-3902. (PMID: 27534817)
Science. 2023 Mar 17;379(6637):1123-1130. (PMID: 36927031)
Virology. 2021 Jun;558:28-37. (PMID: 33714753)
J Immunol. 2023 Nov 15;211(10):1578-1588. (PMID: 37782047)
Immunome Res. 2006 Apr 24;2:2. (PMID: 16635264)
Bioinformatics. 2024 Oct 1;40(10):. (PMID: 39348157)
Proteins. 2006 Oct 1;65(1):40-8. (PMID: 16894596)
Nat Commun. 2019 Jul 3;10(1):2947. (PMID: 31270320)
J Mol Biol. 1994 Aug 26;241(4):534-56. (PMID: 7520084)
Science. 2009 Apr 10;324(5924):246-51. (PMID: 19251591)
Nat Methods. 2022 Jun;19(6):679-682. (PMID: 35637307)
Nat Commun. 2022 Jan 10;13(1):176. (PMID: 35013344)
Bioinformatics. 2021 Sep 29;37(18):3029-3031. (PMID: 33734313)
Patterns (N Y). 2021 Dec 09;3(2):100406. (PMID: 35199061)
Bioinformatics. 2023 Apr 3;39(4):. (PMID: 37039829)
Proteins. 2003 Jul 1;52(1):80-7. (PMID: 12784371)
Dev Comp Immunol. 2003 Jan;27(1):1. (PMID: 12477495)
Nature. 2021 Aug;596(7873):583-589. (PMID: 34265844)
Nat Methods. 2024 Aug;21(8):1514-1524. (PMID: 38744917)
Front Mol Biosci. 2023 Jul 07;10:1214424. (PMID: 37484529)
Nature. 2007 Feb 15;445(7129):732-7. (PMID: 17301785)
J Virol. 2004 Oct;78(19):10724-37. (PMID: 15367639)
Structure. 2004 Feb;12(2):193-204. (PMID: 14962380)
BMC Genomics. 2021 May 31;22(Suppl 2):116. (PMID: 34058977)
Bioinformatics. 2013 Nov 1;29(21):2722-8. (PMID: 23986568)
J Chem Theory Comput. 2023 Aug 22;19(16):5315-5333. (PMID: 37527403)
Nat Commun. 2024 Sep 6;15(1):7785. (PMID: 39242604)
Proteins. 2008 Nov 15;73(3):552-65. (PMID: 18473392)
Biochemistry. 2002 Oct 22;41(42):12729-38. (PMID: 12379115)
J Am Chem Soc. 2003 Feb 19;125(7):1731-7. (PMID: 12580598)
BMC Bioinformatics. 2008 Dec 02;9:514. (PMID: 19055730)
Grant Information: R01AI132668 United States NH NIH HHS; R01AI168459 United States NH NIH HHS; R56 AI155897 United States AI NIAID NIH HHS; R01 AI132668 United States AI NIAID NIH HHS; R56AI155897 United States NH NIH HHS; R01 AI168459 United States AI NIAID NIH HHS
Contributed Indexing: Keywords: AlphaFold2; antibody; computational biology; epitope; immunology; inflammation; systems biology; viruses
Substance Nomenclature: 0 (Epitopes)
0 (Antibodies, Monoclonal)
Entry Date(s): Date Created: 20260918 Date Completed: 20260918 Latest Revision: 20260920
Update Code: 20260920
PubMed Central ID: PMC13588620
DOI: 10.7554/eLife.98369
PMID: 42758531
Βάση Δεδομένων: MEDLINE
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  Data: Linear antibody epitope prediction using AlphaFold2.
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  Data: <searchLink fieldCode="AU" term="%22DeRoo+J%22">DeRoo J</searchLink>; School of Biomedical Engineering, Colorado State University, Fort Collins, United States.<br /><searchLink fieldCode="AU" term="%22Terry+JS%22">Terry JS</searchLink>; Department of Microbiology, Immunology, & Pathology, Colorado State University, Fort Collins, United States.<br /><searchLink fieldCode="AU" term="%22Zhao+N%22">Zhao N</searchLink>; Department of Biochemistry and Molecular Genetics, University of Colorado-Anschutz Medical Campus, Aurora, United States.<br /><searchLink fieldCode="AU" term="%22Stasevich+TJ%22">Stasevich TJ</searchLink>; Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States.<br /><searchLink fieldCode="AU" term="%22Snow+C%22">Snow C</searchLink>; School of Biomedical Engineering, Colorado State University, Fort Collins, United States.; Department of Chemical & Biological Engineering, Colorado State University, Fort Collins, United States.<br /><searchLink fieldCode="AU" term="%22Geiss+BJ%22">Geiss BJ</searchLink>; School of Biomedical Engineering, Colorado State University, Fort Collins, United States.; Department of Microbiology, Immunology, & Pathology, Colorado State University, Fort Collins, United States.
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  Data: Defining the binding epitopes of antibodies is essential for understanding how they bind to their antigens and perform their molecular functions. However, while determining linear epitopes of monoclonal antibodies can be accomplished utilizing well-established empirical procedures, these approaches are generally labor- and time-intensive, and costly. To take advantage of the recent advances in protein structure prediction algorithms available to the scientific community, we developed a calculation pipeline based on the localColabFold implementation of AlphaFold2 that can predict linear antibody epitopes by predicting the structure of the complex between antibody heavy and light chains and target peptide sequences derived from antigens. We found that this AlphaFold2 pipeline, which we call PAbFold, was able to accurately flag known epitope sequences for several well-known antibody targets (HA/Myc) when the target sequence was broken into small overlapping linear peptides and antibody complementarity determining regions were grafted onto several different antibody framework regions in the single-chain antibody fragment format. To determine if this pipeline was able to identify the epitope of a novel antibody with no structural information publicly available, we determined the epitope of a novel anti-SARS-CoV-2 nucleocapsid-targeted antibody using our method and then experimentally validated our computational results using peptide competition ELISA assays. These results indicate that the AlphaFold2-based PAbFold pipeline we developed is capable of accurately identifying linear antibody epitopes in a short time using just antibody and target protein sequences. This emergent capability of the method is sensitive to methodological details such as peptide length, AlphaFold2 neural network versions, and multiple-sequence alignment databases. PAbFold is available at https://github.com/jbderoo/PAbFold.<br /> (© 2024, DeRoo et al.)
– Name: Abstract
  Label: Competing Interests
  Group: Ab
  Data: JD, JT, NZ, CS, BG No competing interests declared, TS Reviewing editor, eLife
– Name: Comment
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  Data: Update of: bioRxiv. 2024 Dec 20:2024.04.19.590298. doi: 10.1101/2024.04.19.590298.. (PMID: <searchLink fieldCode="PM" term="%2238659833%22">38659833)</searchLink>
– Name: Ref
  Label: References
  Group: RefInfo
  Data: Nat Commun. 2023 Apr 25;14(1):2389. (PMID: <searchLink fieldCode="PM" term="%2237185622%22">37185622)</searchLink><br />Nucleic Acids Res. 2000 Jan 1;28(1):214-8. (PMID: <searchLink fieldCode="PM" term="%2210592229%22">10592229)</searchLink><br />Biophys J. 1998 Jul;75(1):422-7. (PMID: <searchLink fieldCode="PM" term="%229649402%22">9649402)</searchLink><br />Nat Protoc. 2023 Jun;18(6):1814-1840. (PMID: <searchLink fieldCode="PM" term="%2237188806%22">37188806)</searchLink><br />J Res Natl Inst Stand Technol. 2019 Oct 09;124:1-6. (PMID: <searchLink fieldCode="PM" term="%2234877177%22">34877177)</searchLink><br />Proteins. 2023 Feb;91(2):171-182. (PMID: <searchLink fieldCode="PM" term="%2236088633%22">36088633)</searchLink><br />Nat Commun. 2024 Aug 10;15(1):6867. (PMID: <searchLink fieldCode="PM" term="%2239127753%22">39127753)</searchLink><br />Front Immunol. 2022 Sep 15;13:960985. (PMID: <searchLink fieldCode="PM" term="%2236189325%22">36189325)</searchLink><br />Structure. 2020 Jan 7;28(1):119-129.e2. (PMID: <searchLink fieldCode="PM" term="%2231727476%22">31727476)</searchLink><br />Curr Opin Struct Biol. 2022 Jun;74:102379. (PMID: <searchLink fieldCode="PM" term="%2235490649%22">35490649)</searchLink><br />Commun Biol. 2023 May 29;6(1):575. (PMID: <searchLink fieldCode="PM" term="%2237248282%22">37248282)</searchLink><br />J Mol Biol. 2016 Oct 9;428(20):3885-3902. (PMID: <searchLink fieldCode="PM" term="%2227534817%22">27534817)</searchLink><br />Science. 2023 Mar 17;379(6637):1123-1130. (PMID: <searchLink fieldCode="PM" term="%2236927031%22">36927031)</searchLink><br />Virology. 2021 Jun;558:28-37. (PMID: <searchLink fieldCode="PM" term="%2233714753%22">33714753)</searchLink><br />J Immunol. 2023 Nov 15;211(10):1578-1588. (PMID: <searchLink fieldCode="PM" term="%2237782047%22">37782047)</searchLink><br />Immunome Res. 2006 Apr 24;2:2. (PMID: <searchLink fieldCode="PM" term="%2216635264%22">16635264)</searchLink><br />Bioinformatics. 2024 Oct 1;40(10):. (PMID: <searchLink fieldCode="PM" term="%2239348157%22">39348157)</searchLink><br />Proteins. 2006 Oct 1;65(1):40-8. (PMID: <searchLink fieldCode="PM" term="%2216894596%22">16894596)</searchLink><br />Nat Commun. 2019 Jul 3;10(1):2947. (PMID: <searchLink fieldCode="PM" term="%2231270320%22">31270320)</searchLink><br />J Mol Biol. 1994 Aug 26;241(4):534-56. (PMID: <searchLink fieldCode="PM" term="%227520084%22">7520084)</searchLink><br />Science. 2009 Apr 10;324(5924):246-51. (PMID: <searchLink fieldCode="PM" term="%2219251591%22">19251591)</searchLink><br />Nat Methods. 2022 Jun;19(6):679-682. (PMID: <searchLink fieldCode="PM" term="%2235637307%22">35637307)</searchLink><br />Nat Commun. 2022 Jan 10;13(1):176. (PMID: <searchLink fieldCode="PM" term="%2235013344%22">35013344)</searchLink><br />Bioinformatics. 2021 Sep 29;37(18):3029-3031. (PMID: <searchLink fieldCode="PM" term="%2233734313%22">33734313)</searchLink><br />Patterns (N Y). 2021 Dec 09;3(2):100406. (PMID: <searchLink fieldCode="PM" term="%2235199061%22">35199061)</searchLink><br />Bioinformatics. 2023 Apr 3;39(4):. (PMID: <searchLink fieldCode="PM" term="%2237039829%22">37039829)</searchLink><br />Proteins. 2003 Jul 1;52(1):80-7. (PMID: <searchLink fieldCode="PM" term="%2212784371%22">12784371)</searchLink><br />Dev Comp Immunol. 2003 Jan;27(1):1. (PMID: <searchLink fieldCode="PM" term="%2212477495%22">12477495)</searchLink><br />Nature. 2021 Aug;596(7873):583-589. (PMID: <searchLink fieldCode="PM" term="%2234265844%22">34265844)</searchLink><br />Nat Methods. 2024 Aug;21(8):1514-1524. (PMID: <searchLink fieldCode="PM" term="%2238744917%22">38744917)</searchLink><br />Front Mol Biosci. 2023 Jul 07;10:1214424. (PMID: <searchLink fieldCode="PM" term="%2237484529%22">37484529)</searchLink><br />Nature. 2007 Feb 15;445(7129):732-7. (PMID: <searchLink fieldCode="PM" term="%2217301785%22">17301785)</searchLink><br />J Virol. 2004 Oct;78(19):10724-37. (PMID: <searchLink fieldCode="PM" term="%2215367639%22">15367639)</searchLink><br />Structure. 2004 Feb;12(2):193-204. (PMID: <searchLink fieldCode="PM" term="%2214962380%22">14962380)</searchLink><br />BMC Genomics. 2021 May 31;22(Suppl 2):116. (PMID: <searchLink fieldCode="PM" term="%2234058977%22">34058977)</searchLink><br />Bioinformatics. 2013 Nov 1;29(21):2722-8. (PMID: <searchLink fieldCode="PM" term="%2223986568%22">23986568)</searchLink><br />J Chem Theory Comput. 2023 Aug 22;19(16):5315-5333. (PMID: <searchLink fieldCode="PM" term="%2237527403%22">37527403)</searchLink><br />Nat Commun. 2024 Sep 6;15(1):7785. (PMID: <searchLink fieldCode="PM" term="%2239242604%22">39242604)</searchLink><br />Proteins. 2008 Nov 15;73(3):552-65. (PMID: <searchLink fieldCode="PM" term="%2218473392%22">18473392)</searchLink><br />Biochemistry. 2002 Oct 22;41(42):12729-38. (PMID: <searchLink fieldCode="PM" term="%2212379115%22">12379115)</searchLink><br />J Am Chem Soc. 2003 Feb 19;125(7):1731-7. (PMID: <searchLink fieldCode="PM" term="%2212580598%22">12580598)</searchLink><br />BMC Bioinformatics. 2008 Dec 02;9:514. (PMID: <searchLink fieldCode="PM" term="%2219055730%22">19055730)</searchLink>
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  Data: <i>Keywords: </i>AlphaFold2; antibody; computational biology; epitope; immunology; inflammation; systems biology; viruses
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