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DINLER AMARAL ANTUNES

TitleProfessor of Computational Biology
Faculty RankAssistant Professor
InstitutionUniversity of Houston
DepartmentBiology and Biochemistry
Address3517 Cullen Blvd. Science & Engineering Research Center (SERC) Bldg 545, Suite 3007.
Houston TX 77004
Phone+17137439427
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Alves CC, Lewis J, Antunes DA, Donadi EA. The Role of Vimentin Peptide Citrullination in the Structure and Dynamics of HLA-DRB1 Rheumatoid Arthritis Risk-Associated Alleles. Int J Mol Sci. 2024 Dec 24; 26(1). PMID: 39795892.
      Citations:    Fields:    Translation:HumansCells
    2. Le HN, de Freitas MV, Antunes DA. Strengths and limitations of web servers for the modeling of TCRpMHC complexes. Comput Struct Biotechnol J. 2024 Dec; 23:2938-2948. PMID: 39104710.
      Citations:    
    3. Wang B, Reville PK, Yassouf MY, Jelloul FZ, Ly C, Desai PN, Wang Z, Borges P, Veletic I, Dasdemir E, Burks JK, Tang G, Guo S, Garza AI, Nasnas C, Vaughn NR, Baran N, Deng Q, Matthews J, Gunaratne PH, Antunes DA, Ekmekcioglu S, Sasaki K, Garcia MB, Cuglievan B, Hao D, Daver N, Green MR, Konopleva M, Futreal A, Post SM, Abbas HA. Comprehensive characterization of IFN? signaling in acute myeloid leukemia reveals prognostic and therapeutic strategies. Nat Commun. 2024 Feb 28; 15(1):1821. PMID: 38418901.
      Citations: 26     Fields:    Translation:Humans
    4. Fasoulis R, Rigo MM, Liz?e G, Antunes DA, Kavraki LE. APE-Gen2.0: Expanding Rapid Class I Peptide-Major Histocompatibility Complex Modeling to Post-Translational Modifications and Noncanonical Peptide Geometries. J Chem Inf Model. 2024 03 11; 64(5):1730-1750. PMID: 38415656.
      Citations: 4     Fields:    Translation:AnimalsCells
    5. 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.
      Citations: 1     Fields:    Translation:Cells
    6. Fasoulis R, Rigo MM, Antunes DA, Paliouras G, Kavraki LE. Transfer learning improves pMHC kinetic stability and immunogenicity predictions. Immunoinformatics (Amst). 2024 Mar; 13. PMID: 38577265.
      Citations:    
    7. Bebis G, Kato M, Kohandel M, Wilkie K, Antunes DA, Chen K, Dou J. Editorial: Advances in mathematical and computational oncology, volume III. Front Oncol. 2023; 13:1282882. PMID: 37817766.
      Citations:    
    8. Antunes DA, Schoeder CT, Baek M, Donadi EA. Editorial: Structural modeling and computational analyses of immune system molecules. Front Immunol. 2023; 14:1274670. PMID: 37731492.
      Citations:    Fields:    
    9. Conev A, Rigo MM, Devaurs D, Fonseca AF, Kalavadwala H, de Freitas MV, Clementi C, Zanatta G, Antunes DA, Kavraki LE. EnGens: a computational framework for generation and analysis of representative protein conformational ensembles. Brief Bioinform. 2023 07 20; 24(4). PMID: 37418278.
      Citations: 10     Fields:    Translation:Cells
    10. Fonseca AF, Antunes DA. CrossDome: an interactive R package to predict cross-reactivity risk using immunopeptidomics databases. Front Immunol. 2023; 14:1142573. PMID: 37377956.
      Citations: 7     Fields:    Translation:HumansCells
    11. Lee SE, Wang F, Grefe M, Trujillo-Ocampo A, Ruiz-Vasquez W, Takahashi K, Abbas HA, Borges P, Antunes DA, Al-Atrash G, Daver N, Molldrem JJ, Futreal A, Garcia-Manero G, Im JS. Immunologic Predictors for Clinical Responses during Immune Checkpoint Blockade in Patients with Myelodysplastic Syndromes. Clin Cancer Res. 2023 05 15; 29(10):1938-1951. PMID: 36988276.
      Citations: 6     Fields:    Translation:Humans
    12. Klein S, Mischke J, Beruldsen F, Prinz I, Antunes DA, Cornberg M, Kraft ARM. Individual Epitope-Specific CD8+ T Cell Immune Responses Are Shaped Differently during Chronic Viral Infection. Pathogens. 2023 May 14; 12(5). PMID: 37242386.
      Citations:    Fields:    
    13. Desai PN, Wang B, Fonseca A, Borges P, Jelloul FZ, Reville PK, Lee E, Ly C, Basi A, Root J, Baran N, Post SM, Deng Q, Sun H, Harmanci AO, Burks JK, Gomez JA, DiNardo CD, Daver NG, Alatrash G, Konopleva M, Green MR, Antunes DA, Futreal A, Hao D, Abbas HA. Single-Cell Profiling of CD8+ T Cells in Acute Myeloid Leukemia Reveals a Continuous Spectrum of Differentiation and Clonal Hyperexpansion. Cancer Immunol Res. 2023 May 10. PMID: 37163233.
      Citations: 20     Fields:    
    14. Hall-Swan S, Slone J, Rigo MM, Antunes DA, Liz?e 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.
      Citations:    Fields:    Translation:Cells
    15. Conev A, Rigo MM, Devaurs D, Fonseca AF, Kalavadwala H, de Freitas MV, Clementi C, Zanatta G, Antunes DA, Kavraki L. EnGens: a computational framework for generation and analysis of representative protein conformational ensembles. bioRxiv. 2023 Apr 28. PMID: 37163076.
      Citations:    
    16. Sonnemann HM, Pazdrak B, Antunes DA, Roszik J, Liz?e G. Vestigial-like 1 (VGLL1): An ancient co-transcriptional activator linking wing, placenta, and tumor development. Biochim Biophys Acta Rev Cancer. 2023 05; 1878(3):188892. PMID: 37004960.
      Citations: 4     Fields:    Translation:HumansAnimals
    17. Alves CC, Arns T, Oliveira ML, Moreau P, Antunes DA, Castelli EC, Mendes-Junior CT, Giuliatti S, Donadi EA. Computational and atomistic studies applied to the understanding of the structural and behavioral features of the immune checkpoint HLA-G molecule and gene. Hum Immunol. 2023 Aug; 84(8):374-383. PMID: 36710086.
      Citations:    Fields:    Translation:Humans
    18. 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, Liz?e G. Charge-based interactions through peptide position 4 drive diversity of antigen presentation by human leukocyte antigen class I molecules. PNAS Nexus. 2022 Jul; 1(3):pgac124. PMID: 36003074.
      Citations:    
    19. 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.
      Citations: 2     Fields:    Translation:HumansCells
    20. Conev A, Devaurs D, Rigo MM, Antunes DA, Kavraki LE. 3pHLA-score improves structure-based peptide-HLA binding affinity prediction. Sci Rep. 2022 06 24; 12(1):10749. PMID: 35750701.
      Citations: 7     Fields:    Translation:HumansCells
    21. Sapoval N, Aghazadeh A, Nute MG, Antunes DA, Balaji A, Baraniuk R, Barberan CJ, Dannenfelser R, Dun C, Edrisi M, Elworth RAL, Kille B, Kyrillidis A, Nakhleh L, Wolfe CR, Yan Z, Yao V, Treangen TJ. Current progress and open challenges for applying deep learning across the biosciences. Nat Commun. 2022 04 01; 13(1):1728. PMID: 35365602.
      Citations: 101     Fields:    
    22. Devaurs D, Antunes DA, Borysik AJ. Computational Modeling of Molecular Structures Guided by Hydrogen-Exchange Data. J Am Soc Mass Spectrom. 2022 Feb 02; 33(2):215-237. PMID: 35077179.
      Citations: 9     Fields:    
    23. Hall-Swan S, Devaurs D, Rigo MM, Antunes DA, Kavraki LE, Zanatta G. DINC-COVID: A webserver for ensemble docking with flexible SARS-CoV-2 proteins. Comput Biol Med. 2021 12; 139:104943. PMID: 34717233.
      Citations: 5     Fields:    
    24. Hall-Swan S, Antunes DA, Devaurs D, Rigo MM, Kavraki LE, Zanatta G. DINC-COVID: A webserver for ensemble docking with flexible SARS-CoV-2 proteins. bioRxiv. 2021 Jan 22. PMID: 33501448.
      Citations:    
    25. Abella JR, Antunes D, Jackson K, Liz?e G, Clementi C, Kavraki LE. Markov state modeling reveals alternative unbinding pathways for peptide-MHC complexes. Proc Natl Acad Sci U S A. 2020 12 01; 117(48):30610-30618. PMID: 33184174.
      Citations: 10     Fields:    Translation:Cells
    26. Arns T, Antunes DA, Abella JR, Rigo MM, Kavraki LE, Giuliatti S, Donadi EA. Structural Modeling and Molecular Dynamics of the Immune Checkpoint Molecule HLA-G. Front Immunol. 2020; 11:575076. PMID: 33240264.
      Citations: 9     Fields:    Translation:HumansCells
    27. Devaurs D, Antunes DA, Kavraki LE. Computational analysis of complement inhibitor compstatin using molecular dynamics. J Mol Model. 2020 Aug 12; 26(9):231. PMID: 32789582.
      Citations: 4     Fields:    Translation:HumansCellsPHPublic Health
    28. Abella JR, Antunes DA, Clementi C, Kavraki LE. Large-Scale Structure-Based Prediction of Stable Peptide Binding to Class I HLAs Using Random Forests. Front Immunol. 2020; 11:1583. PMID: 32793224.
      Citations: 8     Fields:    Translation:HumansCells
    29. Antunes DA, Abella JR, Hall-Swan S, Devaurs D, Conev A, Moll M, Liz?e G, Kavraki LE. HLA-Arena: A Customizable Environment for the Structural Modeling and Analysis of Peptide-HLA Complexes for Cancer Immunotherapy. JCO Clin Cancer Inform. 2020 07; 4:623-636. PMID: 32667823.
      Citations: 15     Fields:    Translation:HumansCells
    30. Devaurs D, Antunes DA, Hall-Swan S, Mitchell N, Moll M, Liz?e G, Kavraki LE. Using parallelized incremental meta-docking can solve the conformational sampling issue when docking large ligands to proteins. BMC Mol Cell Biol. 2019 09 05; 20(1):42. PMID: 31488048.
      Citations: 15     Fields:    Translation:Cells
    31. Soon CF, Zhang S, Suneetha PV, Antunes DA, Manns MP, Raha S, Schultze-Florey C, Prinz I, Wedemeyer H, S?llberg Chen M, Cornberg M. Hepatitis E Virus (HEV)-Specific T Cell Receptor Cross-Recognition: Implications for Immunotherapy. Front Immunol. 2019; 10:2076. PMID: 31552033.
      Citations: 12     Fields:    Translation:HumansCells
    32. Abella JR, Antunes DA, Clementi C, Kavraki LE. APE-Gen: A Fast Method for Generating Ensembles of Bound Peptide-MHC Conformations. Molecules. 2019 Mar 02; 24(5). PMID: 30832312.
      Citations: 25     Fields:    Translation:Cells
    33. Devaurs D, Antunes DA, Kavraki LE. Revealing Unknown Protein Structures Using Computational Conformational Sampling Guided by Experimental Hydrogen-Exchange Data. Int J Mol Sci. 2018 Oct 31; 19(11). PMID: 30384411.
      Citations: 1     Fields:    Translation:HumansCells
    34. Devaurs D, Papanastasiou M, Antunes DA, Abella JR, Moll M, Ricklin D, Lambris JD, Kavraki LE. Native State of Complement Protein C3d Analysed via Hydrogen Exchange and Conformational Sampling. Int J Comput Biol Drug Des. 2018; 11(1-2):90-113. PMID: 30700993.
      Citations: 5     Fields:    
    35. Antunes DA, Devaurs D, Moll M, Liz?e G, Kavraki LE. General Prediction of Peptide-MHC Binding Modes Using Incremental Docking: A Proof of Concept. Sci Rep. 2018 03 12; 8(1):4327. PMID: 29531253.
      Citations: 25     Fields:    Translation:HumansCells
    36. Antunes DA, Abella JR, Devaurs D, Rigo MM, Kavraki LE. Structure-based Methods for Binding Mode and Binding Affinity Prediction for Peptide-MHC Complexes. Curr Top Med Chem. 2018; 18(26):2239-2255. PMID: 30582480.
      Citations: 34     Fields:    Translation:HumansCells
    37. Antunes DA, Moll M, Devaurs D, Jackson KR, Liz?e G, Kavraki LE. DINC 2.0: A New Protein-Peptide Docking Webserver Using an Incremental Approach. Cancer Res. 2017 11 01; 77(21):e55-e57. PMID: 29092940.
      Citations: 44     Fields:    Translation:HumansCells
    38. Antunes DA, Rigo MM, Freitas MV, Mendes MFA, Sinigaglia M, Liz?e 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.
      Citations: 48     Fields:    
    39. Devaurs D, Antunes DA, Papanastasiou M, Moll M, Ricklin D, Lambris JD, Kavraki LE. Coarse-Grained Conformational Sampling of Protein Structure Improves the Fit to Experimental Hydrogen-Exchange Data. Front Mol Biosci. 2017; 4:13. PMID: 28344973.
      Citations:    
    40. Rigo MM, Antunes DA, Vaz de Freitas M, Fabiano de Almeida Mendes M, Meira L, Sinigaglia M, Vieira GF. DockTope: a Web-based tool for automated pMHC-I modelling. Sci Rep. 2015 Dec 17; 5:18413. PMID: 26674250.
      Citations: 31     Fields:    Translation:HumansCells
    41. Antunes DA, Devaurs D, Kavraki LE. Understanding the challenges of protein flexibility in drug design. Expert Opin Drug Discov. 2015 Dec; 10(12):1301-13. PMID: 26414598.
      Citations: 54     Fields:    Translation:HumansCells
    42. Mendes MF, Antunes DA, Rigo MM, Sinigaglia M, Vieira GF. Improved structural method for T-cell cross-reactivity prediction. Mol Immunol. 2015 Oct; 67(2 Pt B):303-10. PMID: 26141239.
      Citations: 20     Fields:    Translation:HumansCells
    43. Zhang S, Bakshi RK, Suneetha PV, Fytili P, Antunes DA, Vieira GF, Jacobs R, Klade CS, Manns MP, Kraft AR, Wedemeyer H, Schlaphoff V, Cornberg M. 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 Aug; 89(16):8304-17. PMID: 26041301.
      Citations: 21     Fields:    Translation:HumansCells
    44. Figueiredo DF, Antunes DA, Rigo MM, Mendes MF, Silva JP, Mayer FQ, Matte U, Giugliani R, Vieira GF, Sinigaglia M. Lessons from molecular modeling human a-L-iduronidase. J Mol Graph Model. 2014 Nov; 54:107-13. PMID: 25459762.
      Citations:    Fields:    Translation:HumansCells
    45. Antunes DA, Rigo MM, Sinigaglia M, de Medeiros RM, Junqueira DM, Almeida SE, Vieira GF. New insights into the in silico prediction of HIV protease resistance to nelfinavir. PLoS One. 2014; 9(1):e87520. PMID: 24498124.
      Citations: 9     Fields:    Translation:HumansCells
    46. Sinigaglia M, Antunes DA, Rigo MM, Chies JA, Vieira GF. CrossTope: a curate repository of 3D structures of immunogenic peptide: MHC complexes. Database (Oxford). 2013; 2013:bat002. PMID: 23396301.
      Citations: 13     Fields:    Translation:HumansAnimals
    47. Rigo MM, Antunes DA, Cibulski SP, Sinigaglia M, Chies JA, Vieira GF. Immunogenic epitopes of Hantaviruses' N protein are restricted to conserved regions. Front Biosci (Landmark Ed). 2012 01 01; 17(4):1582-8. PMID: 22201821.
      Citations: 3     Fields:    Translation:HumansCells
    48. 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 Jul; 48(12-13):1461-7. PMID: 21513985.
      Citations: 16     Fields:    Translation:HumansCells
    49. Antunes DA, Vieira GF, Rigo MM, Cibulski SP, Sinigaglia M, Chies JA. Structural allele-specific patterns adopted by epitopes in the MHC-I cleft and reconstruction of MHC:peptide complexes to cross-reactivity assessment. PLoS One. 2010 Apr 26; 5(4):e10353. PMID: 20442757.
      Citations: 13     Fields:    Translation:HumansCells
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