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For: Antunes DA, Rigo MM, Silva JP, Cibulski SP, Sinigaglia M, Chies JA, Vieira GF. Structural in silico analysis of cross-genotype-reactivity among naturally occurring HCV NS3-1073-variants in the context of HLA-A*02:01 allele. Mol Immunol 2011;48:1461-7. [DOI: 10.1016/j.molimm.2011.03.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Revised: 02/15/2011] [Accepted: 03/28/2011] [Indexed: 12/17/2022]
Number Cited by Other Article(s)
1
Antunes DA, Baker BM, Cornberg M, Selin LK. Editorial: Quantification and prediction of T-cell cross-reactivity through experimental and computational methods. Front Immunol 2024;15:1377259. [PMID: 38444853 PMCID: PMC10912571 DOI: 10.3389/fimmu.2024.1377259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 02/05/2024] [Indexed: 03/07/2024]  Open
2
Fonseca AF, Antunes DA. CrossDome: an interactive R package to predict cross-reactivity risk using immunopeptidomics databases. Front Immunol 2023;14:1142573. [PMID: 37377956 PMCID: PMC10291144 DOI: 10.3389/fimmu.2023.1142573] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023]  Open
3
Hall-Swan S, Slone J, Rigo MM, Antunes DA, Lizée G, Kavraki LE. PepSim: T-cell cross-reactivity prediction via comparison of peptide sequence and peptide-HLA structure. Front Immunol 2023;14:1108303. [PMID: 37187737 PMCID: PMC10175663 DOI: 10.3389/fimmu.2023.1108303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 04/12/2023] [Indexed: 05/17/2023]  Open
4
Saotome K, Dudgeon D, Colotti K, Moore MJ, Jones J, Zhou Y, Rafique A, Yancopoulos GD, Murphy AJ, Lin JC, Olson WC, Franklin MC. Structural analysis of cancer-relevant TCR-CD3 and peptide-MHC complexes by cryoEM. Nat Commun 2023;14:2401. [PMID: 37100770 PMCID: PMC10132440 DOI: 10.1038/s41467-023-37532-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 03/21/2023] [Indexed: 04/28/2023]  Open
5
Rigo MM, Fasoulis R, Conev A, Hall-Swan S, Antunes DA, Kavraki LE. SARS-Arena: Sequence and Structure-Guided Selection of Conserved Peptides from SARS-related Coronaviruses for Novel Vaccine Development. Front Immunol 2022;13:931155. [PMID: 35903104 PMCID: PMC9315150 DOI: 10.3389/fimmu.2022.931155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/10/2022] [Indexed: 02/01/2023]  Open
6
Jackson KR, Antunes DA, Talukder AH, Maleki AR, Amagai K, Salmon A, Katailiha AS, Chiu Y, Fasoulis R, Rigo MM, Abella JR, Melendez BD, Li F, Sun Y, Sonnemann HM, Belousov V, Frenkel F, Justesen S, Makaju A, Liu Y, Horn D, Lopez-Ferrer D, Huhmer AF, Hwu P, Roszik J, Hawke D, Kavraki LE, Lizée G. Charge-based interactions through peptide position 4 drive diversity of antigen presentation by human leukocyte antigen class I molecules. PNAS NEXUS 2022;1:pgac124. [PMID: 36003074 PMCID: PMC9391200 DOI: 10.1093/pnasnexus/pgac124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
7
Balz K, Trassl L, Härtel V, Nelson PP, Skevaki C. Virus-Induced T Cell-Mediated Heterologous Immunity and Vaccine Development. Front Immunol 2020;11:513. [PMID: 32296430 PMCID: PMC7137989 DOI: 10.3389/fimmu.2020.00513] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 03/06/2020] [Indexed: 12/15/2022]  Open
8
Vianna P, Mendes MF, Bragatte MA, Ferreira PS, Salzano FM, Bonamino MH, Vieira GF. pMHC Structural Comparisons as a Pivotal Element to Detect and Validate T-Cell Targets for Vaccine Development and Immunotherapy-A New Methodological Proposal. Cells 2019;8:cells8121488. [PMID: 31766602 PMCID: PMC6952977 DOI: 10.3390/cells8121488] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 11/15/2019] [Accepted: 11/16/2019] [Indexed: 12/02/2022]  Open
9
Meireles MR, Bragatte MAS, Bandinelli E, Salzano FM, Vieira GF. A new in silico approach to investigate molecular aspects of factor IX missense causative mutations and their impact on the hemophilia B severity. Hum Mutat 2019;40:706-715. [PMID: 30817849 DOI: 10.1002/humu.23733] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 01/23/2019] [Accepted: 02/23/2019] [Indexed: 11/10/2022]
10
Abella JR, Antunes DA, Clementi C, Kavraki LE. APE-Gen: A Fast Method for Generating Ensembles of Bound Peptide-MHC Conformations. Molecules 2019;24:E881. [PMID: 30832312 PMCID: PMC6429480 DOI: 10.3390/molecules24050881] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 02/26/2019] [Accepted: 02/27/2019] [Indexed: 11/16/2022]  Open
11
Antunes DA, Devaurs D, Moll M, Lizée G, Kavraki LE. General Prediction of Peptide-MHC Binding Modes Using Incremental Docking: A Proof of Concept. Sci Rep 2018. [PMID: 29531253 PMCID: PMC5847594 DOI: 10.1038/s41598-018-22173-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]  Open
12
Antunes DA, Rigo MM, Freitas MV, Mendes MFA, Sinigaglia M, Lizée G, Kavraki LE, Selin LK, Cornberg M, Vieira GF. Interpreting T-Cell Cross-reactivity through Structure: Implications for TCR-Based Cancer Immunotherapy. Front Immunol 2017;8:1210. [PMID: 29046675 PMCID: PMC5632759 DOI: 10.3389/fimmu.2017.01210] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 09/12/2017] [Indexed: 12/16/2022]  Open
13
Hepatitis C virus infection from the perspective of heterologous immunity. Curr Opin Virol 2016;16:41-48. [DOI: 10.1016/j.coviro.2016.01.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 01/08/2016] [Indexed: 01/14/2023]
14
DockTope: a Web-based tool for automated pMHC-I modelling. Sci Rep 2015;5:18413. [PMID: 26674250 PMCID: PMC4682062 DOI: 10.1038/srep18413] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 11/18/2015] [Indexed: 11/08/2022]  Open
15
Kenney LL, Cornberg M, Chen AT, Emonet S, de la Torre JC, Selin LK. Increased Immune Response Variability during Simultaneous Viral Coinfection Leads to Unpredictability in CD8 T Cell Immunity and Pathogenesis. J Virol 2015;89:10786-801. [PMID: 26269191 PMCID: PMC4621125 DOI: 10.1128/jvi.01432-15] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 08/07/2015] [Indexed: 12/11/2022]  Open
16
Gil A, Kenney LL, Mishra R, Watkin LB, Aslan N, Selin LK. Vaccination and heterologous immunity: educating the immune system. Trans R Soc Trop Med Hyg 2015;109:62-9. [PMID: 25573110 DOI: 10.1093/trstmh/tru198] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]  Open
17
Improved structural method for T-cell cross-reactivity prediction. Mol Immunol 2015;67:303-10. [PMID: 26141239 DOI: 10.1016/j.molimm.2015.06.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 06/03/2015] [Accepted: 06/16/2015] [Indexed: 10/23/2022]
18
Frequency, Private Specificity, and Cross-Reactivity of Preexisting Hepatitis C Virus (HCV)-Specific CD8+ T Cells in HCV-Seronegative Individuals: Implications for Vaccine Responses. J Virol 2015;89:8304-17. [PMID: 26041301 DOI: 10.1128/jvi.00539-15] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 05/22/2015] [Indexed: 12/28/2022]  Open
19
Databases for T-cell epitopes. Methods Mol Biol 2015;1184:123-34. [PMID: 25048121 DOI: 10.1007/978-1-4939-1115-8_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
20
Sinigaglia M, Antunes DA, Rigo MM, Chies JAB, Vieira GF. CrossTope: a curate repository of 3D structures of immunogenic peptide: MHC complexes. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2013;2013:bat002. [PMID: 23396301 PMCID: PMC3567486 DOI: 10.1093/database/bat002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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