ANTUNES, DINLER
first name: DINLER
last name: ANTUNES
full name: DINLER AMARAL ANTUNES
has faculty rank: Assistant Professor
has network: research areas
has network: similar to
has network: selected publications
Person ID: 2398279
person in primary position: Professor of Computational Biology
similar to: Leszczynski, Jerzy
similar to: Holford, Mandë
similar to: Matsui, Hiroshi
similar to: Lazaridis, Themis
similar to: Sullivan, Kathleen
type: Agent
type: Person
selected publications: Authorship 84112
selected publications: Authorship 87132
selected publications: Authorship 87940
selected publications: Authorship 88989
selected publications: Authorship 85662
selected publications: Authorship 82600
selected publications: Authorship 85892
selected publications: Authorship 84801
selected publications: Authorship 86113
selected publications: Authorship 81577
selected publications: Authorship 84546
selected publications: Authorship 88240
selected publications: Authorship 85422
selected publications: Authorship 86321
selected publications: Authorship 87221
selected publications: Authorship 83154
selected publications: Authorship 83139
selected publications: Authorship 86947
selected publications: Authorship 86430
selected publications: Authorship 88295
selected publications: Authorship 87942
selected publications: Authorship 88810
selected publications: Authorship 87541
selected publications: Authorship 82202
selected publications: Authorship 87352
selected publications: Authorship 89149
selected publications: Authorship 88147
selected publications: Authorship 82869
selected publications: Authorship 82937
selected publications: Authorship 83674
selected publications: Authorship 86835
selected publications: Authorship 86040
selected publications: Authorship 85638
selected publications: Authorship 87012
selected publications: Authorship 86935
selected publications: Authorship 84488
selected publications: Authorship 87318
selected publications: Authorship 82818
selected publications: Authorship 85188
selected publications: Authorship 89701
selected publications: Authorship 87140
selected publications: Authorship 89308
selected publications: Authorship 88506
selected publications: Authorship 88030
selected publications: Authorship 85645
selected publications: Authorship 83614
selected publications: Authorship 84943
selected publications: Authorship 82615
selected publications: Authorship 82653
research areas: Peptides
research areas: Histocompatibility Antigens Class I
research areas: Proteins
research areas: T-Lymphocytes
research areas: Receptors, Antigen, T-Cell
mailing address: http://connect.rtrn.net/profiles/profile/21595537
middle name or initial: AMARAL
positions: Professor of Computational Biology
phone: +17137439427
preferred title: Professor of Computational Biology

Assistant Professor
sort order: 14
type: Faculty Rank

Associate Professor
sort order: 31
type: Faculty Rank

Professor
sort order: 91
type: Faculty Rank

http://connect.rtrn.net/profiles/profile/21595537
type: Address
address line 1: 3517 Cullen Blvd. Science & Engineering Research Center (SERC) Bldg 545, Suite 3007.
city: Houston
postal code: 77004
state or province: TX

Assistant Professor of Chemistry
is primary position: true
position in department: chemistry
sort order: 1
type: Position
HR job title: Assistant Professor of Chemistry
position in organization: Hunter College, CUNY

Professor of Chemistry
is primary position: true
position in department: chemistry
sort order: 1
type: Position
HR job title: Professor of Chemistry
position in organization: Hunter College, CUNY

Professor of Chemistry, ICN Director
is primary position: true
position in department: Chemistry and Biochemistry
sort order: 1
type: Position
HR job title: Professor of Chemistry, ICN Director
position in organization: Jackson State University

APRN, PMHCNS-BC
is primary position: true
position in department: Nursing
position in division: http://connect.rtrn.net/profiles/profile/887633
sort order: 1
type: Position
HR job title: APRN, PMHCNS-BC
position in organization: University of Hawaii at Manoa

Professor of Computational Biology
is primary position: true
position in department: Biology and Biochemistry
position in division: Biochemistry
sort order: 1
type: Position
HR job title: Professor of Computational Biology
position in organization: University of Houston

Professor
is primary position: true
position in department: Chemistry and Biochemistry
position in division: Division of Science
sort order: 1
type: Position
HR job title: Professor
position in organization: City College, CUNY

Division of Science
type: Division
type: Organization

research areas
maximum weight: 3.45638
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number of connections: 120
predicate node: http://connect.rtrn.net/profiles/profile/198
predicate: research areas
type: Network

similar to
maximum weight: 28.6276
minimum weight: 3.46213
number of connections: 60
predicate node: http://connect.rtrn.net/profiles/profile/506
predicate: similar to
type: Network

selected publications
maximum weight: 1
minimum weight: 1
number of connections: 49
predicate node: http://connect.rtrn.net/profiles/profile/94
predicate: selected publications
type: Network

Authorship 82818
type: Authorship
author rank in publication: 1
linked author: ANTUNES, DINLER
linked information resource: Interpreting T-Cell Cross-reactivity through Structure: Implications for TCR-Based Cancer Immunotherapy.

Authorship 82869
type: Authorship
author rank in publication: 2
linked author: ANTUNES, DINLER
linked information resource: Large-Scale Structure-Based Prediction of Stable Peptide Binding to Class I HLAs Using Random Forests.

Authorship 83154
type: Authorship
author rank in publication: 3
linked author: ANTUNES, DINLER
linked information resource: Vestigial-like 1 (VGLL1): An ancient co-transcriptional activator linking wing, placenta, and tumor development.

Authorship 84546
type: Authorship
author rank in publication: 9
linked author: ANTUNES, DINLER
linked information resource: Immunologic Predictors for Clinical Responses during Immune Checkpoint Blockade in Patients with Myelodysplastic Syndromes.

Authorship 85422
type: Authorship
author rank in publication: 23
linked author: ANTUNES, DINLER
linked information resource: Single-Cell Profiling of CD8+ T Cells in Acute Myeloid Leukemia Reveals a Continuous Spectrum of Differentiation and Clonal Hyperexpansion.

Authorship 85638
type: Authorship
author rank in publication: 2
linked author: ANTUNES, DINLER
linked information resource: Revealing Unknown Protein Structures Using Computational Conformational Sampling Guided by Experimental Hydrogen-Exchange Data.

Authorship 86430
type: Authorship
author rank in publication: 5
linked author: ANTUNES, DINLER
linked information resource: SARS-Arena: Sequence and Structure-Guided Selection of Conserved Peptides from SARS-related Coronaviruses for Novel Vaccine Development.

Authorship 86835
type: Authorship
author rank in publication: 4
linked author: ANTUNES, DINLER
linked information resource: Hepatitis E Virus (HEV)-Specific T Cell Receptor Cross-Recognition: Implications for Immunotherapy.

Authorship 86935
type: Authorship
author rank in publication: 1
linked author: ANTUNES, DINLER
linked information resource: General Prediction of Peptide-MHC Binding Modes Using Incremental Docking: A Proof of Concept.

Authorship 86947
type: Authorship
author rank in publication: 2
linked author: ANTUNES, DINLER
linked information resource: Charge-based interactions through peptide position 4 drive diversity of antigen presentation by human leukocyte antigen class I molecules.

Authorship 87012
type: Authorship
author rank in publication: 3
linked author: ANTUNES, DINLER
linked information resource: Native State of Complement Protein C3d Analysed via Hydrogen Exchange and Conformational Sampling.

Authorship 87132
type: Authorship
author rank in publication: 3
linked author: ANTUNES, DINLER
linked information resource: Strengths and limitations of web servers for the modeling of TCRpMHC complexes.

Authorship 87221
type: Authorship
author rank in publication: 4
linked author: ANTUNES, DINLER
linked information resource: PepSim: T-cell cross-reactivity prediction via comparison of peptide sequence and peptide-HLA structure.

Authorship 87318
type: Authorship
author rank in publication: 1
linked author: ANTUNES, DINLER
linked information resource: DINC 2.0: A New Protein-Peptide Docking Webserver Using an Incremental Approach.

Authorship 87352
type: Authorship
author rank in publication: 2
linked author: ANTUNES, DINLER
linked information resource: Markov state modeling reveals alternative unbinding pathways for peptide-MHC complexes.

Authorship 87940
type: Authorship
author rank in publication: 21
linked author: ANTUNES, DINLER
linked information resource: Comprehensive characterization of IFN? signaling in acute myeloid leukemia reveals prognostic and therapeutic strategies.

Authorship 87942
type: Authorship
author rank in publication: 4
linked author: ANTUNES, DINLER
linked information resource: Current progress and open challenges for applying deep learning across the biosciences.

Authorship 88240
type: Authorship
author rank in publication: 5
linked author: ANTUNES, DINLER
linked information resource: Individual Epitope-Specific CD8+ T Cell Immune Responses Are Shaped Differently during Chronic Viral Infection.

Authorship 88295
type: Authorship
author rank in publication: 4
linked author: ANTUNES, DINLER
linked information resource: 3pHLA-score improves structure-based peptide-HLA binding affinity prediction.

Authorship 88810
type: Authorship
author rank in publication: 2
linked author: ANTUNES, DINLER
linked information resource: Computational Modeling of Molecular Structures Guided by Hydrogen-Exchange Data.

Authorship 88989
type: Authorship
author rank in publication: 4
linked author: ANTUNES, DINLER
linked information resource: APE-Gen2.0: Expanding Rapid Class I Peptide-Major Histocompatibility Complex Modeling to Post-Translational Modifications and Noncanonical Peptide Geometries.

Authorship 89149
type: Authorship
author rank in publication: 2
linked author: ANTUNES, DINLER
linked information resource: Structural Modeling and Molecular Dynamics of the Immune Checkpoint Molecule HLA-G.

Authorship 89308
type: Authorship
author rank in publication: 2
linked author: ANTUNES, DINLER
linked information resource: Improved structural method for T-cell cross-reactivity prediction.

Authorship 89701
type: Authorship
author rank in publication: 2
linked author: ANTUNES, DINLER
linked information resource: DockTope: a Web-based tool for automated pMHC-I modelling.

Authorship 82202
type: Authorship
author rank in publication: 2
linked author: ANTUNES, DINLER
linked information resource: DINC-COVID: A webserver for ensemble docking with flexible SARS-CoV-2 proteins.

Authorship 82600
type: Authorship
author rank in publication: 3
linked author: ANTUNES, DINLER
linked information resource: Transfer learning improves pMHC kinetic stability and immunogenicity predictions.

Authorship 82653
type: Authorship
author rank in publication: 1
linked author: ANTUNES, DINLER
linked information resource: Structural allele-specific patterns adopted by epitopes in the MHC-I cleft and reconstruction of MHC:peptide complexes to cross-reactivity assessment.

Authorship 82937
type: Authorship
author rank in publication: 1
linked author: ANTUNES, DINLER
linked information resource: HLA-Arena: A Customizable Environment for the Structural Modeling and Analysis of Peptide-HLA Complexes for Cancer Immunotherapy.

Authorship 83139
type: Authorship
author rank in publication: 5
linked author: ANTUNES, DINLER
linked information resource: Computational and atomistic studies applied to the understanding of the structural and behavioral features of the immune checkpoint HLA-G molecule and gene.

Authorship 83614
type: Authorship
author rank in publication: 2
linked author: ANTUNES, DINLER
linked information resource: CrossTope: a curate repository of 3D structures of immunogenic peptide: MHC complexes.

Authorship 84488
type: Authorship
author rank in publication: 1
linked author: ANTUNES, DINLER
linked information resource: Structure-based Methods for Binding Mode and Binding Affinity Prediction for Peptide-MHC Complexes.

Authorship 84943
type: Authorship
author rank in publication: 2
linked author: ANTUNES, DINLER
linked information resource: Immunogenic epitopes of Hantaviruses' N protein are restricted to conserved regions.

Authorship 85188
type: Authorship
author rank in publication: 2
linked author: ANTUNES, DINLER
linked information resource: Coarse-Grained Conformational Sampling of Protein Structure Improves the Fit to Experimental Hydrogen-Exchange Data.

Authorship 85645
type: Authorship
author rank in publication: 1
linked author: ANTUNES, DINLER
linked information resource: New insights into the in silico prediction of HIV protease resistance to nelfinavir.

Authorship 85892
type: Authorship
author rank in publication: 5
linked author: ANTUNES, DINLER
linked information resource: Editorial: Advances in mathematical and computational oncology, volume III.

Authorship 86321
type: Authorship
author rank in publication: 9
linked author: ANTUNES, DINLER
linked information resource: EnGens: a computational framework for generation and analysis of representative protein conformational ensembles.

Authorship 87140
type: Authorship
author rank in publication: 1
linked author: ANTUNES, DINLER
linked information resource: Understanding the challenges of protein flexibility in drug design.

Authorship 88506
type: Authorship
author rank in publication: 5
linked author: ANTUNES, DINLER
linked information resource: Frequency, Private Specificity, and Cross-Reactivity of Preexisting Hepatitis C Virus (HCV)-Specific CD8+ T Cells in HCV-Seronegative Individuals: Implications for Vaccine Responses.

Authorship 81577
type: Authorship
author rank in publication: 2
linked author: ANTUNES, DINLER
linked information resource: CrossDome: an interactive R package to predict cross-reactivity risk using immunopeptidomics databases.

Authorship 82615
type: Authorship
author rank in publication: 1
linked author: ANTUNES, DINLER
linked information resource: Structural in silico analysis of cross-genotype-reactivity among naturally occurring HCV NS3-1073-variants in the context of HLA-A*02:01 allele.

Authorship 83674
type: Authorship
author rank in publication: 2
linked author: ANTUNES, DINLER
linked information resource: Using parallelized incremental meta-docking can solve the conformational sampling issue when docking large ligands to proteins.

Authorship 84112
type: Authorship
author rank in publication: 3
linked author: ANTUNES, DINLER
linked information resource: The Role of Vimentin Peptide Citrullination in the Structure and Dynamics of HLA-DRB1 Rheumatoid Arthritis Risk-Associated Alleles.

Authorship 84801
type: Authorship
author rank in publication: 1
linked author: ANTUNES, DINLER
linked information resource: Editorial: Structural modeling and computational analyses of immune system molecules.

Authorship 85662
type: Authorship
author rank in publication: 1
linked author: ANTUNES, DINLER
linked information resource: Editorial: Quantification and prediction of T-cell cross-reactivity through experimental and computational methods.

Authorship 86040
type: Authorship
author rank in publication: 2
linked author: ANTUNES, DINLER
linked information resource: APE-Gen: A Fast Method for Generating Ensembles of Bound Peptide-MHC Conformations.

Authorship 86113
type: Authorship
author rank in publication: 9
linked author: ANTUNES, DINLER
linked information resource: EnGens: a computational framework for generation and analysis of representative protein conformational ensembles.

Authorship 87541
type: Authorship
author rank in publication: 4
linked author: ANTUNES, DINLER
linked information resource: DINC-COVID: A webserver for ensemble docking with flexible SARS-CoV-2 proteins.

Authorship 88030
type: Authorship
author rank in publication: 2
linked author: ANTUNES, DINLER
linked information resource: Lessons from molecular modeling human a-L-iduronidase.

Authorship 88147
type: Authorship
author rank in publication: 2
linked author: ANTUNES, DINLER
linked information resource: Computational analysis of complement inhibitor compstatin using molecular dynamics.

PepSim: T-cell cross-reactivity prediction via comparison of peptide sequence and peptide-HLA structure.
PubMed Identifier: 37187737
author list: Hall-Swan S, Slone J, Rigo MM, Antunes DA, Liz?e G, Kavraki LE
published in: Frontiers in immunology
information resource reference: 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.
journal title abbreviation: Front Immunol
publication date: 2023-04-28T00:00:00
year: 2023
type: Academic Article
type: Article
type: Document
type: Information Resource

Hepatitis E Virus (HEV)-Specific T Cell Receptor Cross-Recognition: Implications for Immunotherapy.
PubMed Identifier: 31552033
author list: 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
published in: Frontiers in immunology
information resource reference: 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.
journal title abbreviation: Front Immunol
publication date: 2019-09-04T00:00:00
year: 2019
type: Academic Article
type: Article
type: Document
type: Information Resource

DINC-COVID: A webserver for ensemble docking with flexible SARS-CoV-2 proteins.
PubMed Identifier: 33501448
author list: Hall-Swan S, Antunes DA, Devaurs D, Rigo MM, Kavraki LE, Zanatta G
published in: bioRxiv : the preprint server for biology
information resource reference: 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.
journal title abbreviation: bioRxiv
publication date: 2021-01-22T00:00:00
year: 2021
type: Academic Article
type: Article
type: Document
type: Information Resource

Structural Modeling and Molecular Dynamics of the Immune Checkpoint Molecule HLA-G.
PubMed Identifier: 33240264
author list: Arns T, Antunes DA, Abella JR, Rigo MM, Kavraki LE, Giuliatti S, Donadi EA
published in: Frontiers in immunology
information resource reference: 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.
journal title abbreviation: Front Immunol
publication date: 2020-11-06T00:00:00
year: 2020
type: Academic Article
type: Article
type: Document
type: Information Resource

APE-Gen2.0: Expanding Rapid Class I Peptide-Major Histocompatibility Complex Modeling to Post-Translational Modifications and Noncanonical Peptide Geometries.
PubMed Identifier: 38415656
author list: Fasoulis R, Rigo MM, Liz?e G, Antunes DA, Kavraki LE
published in: Journal of chemical information and modeling
information resource reference: 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.
journal title abbreviation: J Chem Inf Model
publication date: 2024-02-28T00:00:00
year: 2024
type: Academic Article
type: Article
type: Document
type: Information Resource

Editorial: Quantification and prediction of T-cell cross-reactivity through experimental and computational methods.
PubMed Identifier: 38444853
author list: Antunes DA, Baker BM, Cornberg M, Selin LK
published in: Frontiers in immunology
information resource reference: 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.
journal title abbreviation: Front Immunol
publication date: 2024-02-20T00:00:00
year: 2024
type: Academic Article
type: Article
type: Document
type: Information Resource

Editorial: Advances in mathematical and computational oncology, volume III.
PubMed Identifier: 37817766
author list: Bebis G, Kato M, Kohandel M, Wilkie K, Antunes DA, Chen K, Dou J
published in: Frontiers in oncology
information resource reference: 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.
journal title abbreviation: Front Oncol
publication date: 2023-09-25T00:00:00
year: 2023
type: Academic Article
type: Article
type: Document
type: Information Resource

Structural in silico analysis of cross-genotype-reactivity among naturally occurring HCV NS3-1073-variants in the context of HLA-A*02:01 allele.
PubMed Identifier: 21513985
author list: Antunes DA, Rigo MM, Silva JP, Cibulski SP, Sinigaglia M, Chies JA, Vieira GF
published in: Molecular immunology
information resource reference: 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.
journal title abbreviation: Mol Immunol
publication date: 2011-04-21T00:00:00
year: 2011
type: Academic Article
type: Article
type: Document
type: Information Resource

Comprehensive characterization of IFN? signaling in acute myeloid leukemia reveals prognostic and therapeutic strategies.
PubMed Identifier: 38418901
author list: 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
published in: Nature communications
information resource reference: 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.
journal title abbreviation: Nat Commun
publication date: 2024-02-28T00:00:00
year: 2024
type: Academic Article
type: Article
type: Document
type: Information Resource

Transfer learning improves pMHC kinetic stability and immunogenicity predictions.
PubMed Identifier: 38577265
author list: Fasoulis R, Rigo MM, Antunes DA, Paliouras G, Kavraki LE
published in: Immunoinformatics (Amsterdam, Netherlands)
information resource reference: Fasoulis R, Rigo MM, Antunes DA, Paliouras G, Kavraki LE. Transfer learning improves pMHC kinetic stability and immunogenicity predictions. Immunoinformatics (Amst). 2024 Mar; 13.
journal title abbreviation: Immunoinformatics (Amst)
publication date: 2023-12-21T00:00:00
year: 2023
type: Academic Article
type: Article
type: Document
type: Information Resource

Structural allele-specific patterns adopted by epitopes in the MHC-I cleft and reconstruction of MHC:peptide complexes to cross-reactivity assessment.
PubMed Identifier: 20442757
author list: Antunes DA, Vieira GF, Rigo MM, Cibulski SP, Sinigaglia M, Chies JA
published in: PloS one
information resource reference: 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.
journal title abbreviation: PLoS One
publication date: 2010-04-26T00:00:00
year: 2010
type: Academic Article
type: Article
type: Document
type: Information Resource

Immunogenic epitopes of Hantaviruses' N protein are restricted to conserved regions.
PubMed Identifier: 22201821
author list: Rigo MM, Antunes DA, Cibulski SP, Sinigaglia M, Chies JA, Vieira GF
published in: Frontiers in bioscience (Landmark edition)
information resource reference: 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.
journal title abbreviation: Front Biosci (Landmark Ed)
publication date: 2012-01-01T00:00:00
year: 2012
type: Academic Article
type: Article
type: Document
type: Information Resource

Understanding the challenges of protein flexibility in drug design.
PubMed Identifier: 26414598
author list: Antunes DA, Devaurs D, Kavraki LE
published in: Expert opinion on drug discovery
information resource reference: 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.
journal title abbreviation: Expert Opin Drug Discov
publication date: 2015-09-28T00:00:00
year: 2015
type: Academic Article
type: Article
type: Document
type: Information Resource

CrossTope: a curate repository of 3D structures of immunogenic peptide: MHC complexes.
PubMed Identifier: 23396301
author list: Sinigaglia M, Antunes DA, Rigo MM, Chies JA, Vieira GF
published in: Database : the journal of biological databases and curation
information resource reference: 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.
journal title abbreviation: Database (Oxford)
publication date: 2013-02-08T00:00:00
year: 2013
type: Academic Article
type: Article
type: Document
type: Information Resource

Immunologic Predictors for Clinical Responses during Immune Checkpoint Blockade in Patients with Myelodysplastic Syndromes.
PubMed Identifier: 36988276
author list: 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
published in: Clinical cancer research : an official journal of the American Association for Cancer Research
information resource reference: 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.
journal title abbreviation: Clin Cancer Res
publication date: 2023-05-15T00:00:00
year: 2023
type: Academic Article
type: Article
type: Document
type: Information Resource

EnGens: a computational framework for generation and analysis of representative protein conformational ensembles.
PubMed Identifier: 37163076
author list: Conev A, Rigo MM, Devaurs D, Fonseca AF, Kalavadwala H, de Freitas MV, Clementi C, Zanatta G, Antunes DA, Kavraki L
published in: bioRxiv : the preprint server for biology
information resource reference: 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.
journal title abbreviation: bioRxiv
publication date: 2023-04-28T00:00:00
year: 2023
type: Academic Article
type: Article
type: Document
type: Information Resource

CrossDome: an interactive R package to predict cross-reactivity risk using immunopeptidomics databases.
PubMed Identifier: 37377956
author list: Fonseca AF, Antunes DA
published in: Frontiers in immunology
information resource reference: Fonseca AF, Antunes DA. CrossDome: an interactive R package to predict cross-reactivity risk using immunopeptidomics databases. Front Immunol. 2023; 14:1142573.
journal title abbreviation: Front Immunol
publication date: 2023-06-12T00:00:00
year: 2023
type: Academic Article
type: Article
type: Document
type: Information Resource

EnGens: a computational framework for generation and analysis of representative protein conformational ensembles.
PubMed Identifier: 37418278
author list: Conev A, Rigo MM, Devaurs D, Fonseca AF, Kalavadwala H, de Freitas MV, Clementi C, Zanatta G, Antunes DA, Kavraki LE
published in: Briefings in bioinformatics
information resource reference: 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).
journal title abbreviation: Brief Bioinform
publication date: 2023-07-20T00:00:00
year: 2023
type: Academic Article
type: Article
type: Document
type: Information Resource

Editorial: Structural modeling and computational analyses of immune system molecules.
PubMed Identifier: 37731492
author list: Antunes DA, Schoeder CT, Baek M, Donadi EA
published in: Frontiers in immunology
information resource reference: Antunes DA, Schoeder CT, Baek M, Donadi EA. Editorial: Structural modeling and computational analyses of immune system molecules. Front Immunol. 2023; 14:1274670.
journal title abbreviation: Front Immunol
publication date: 2023-09-05T00:00:00
year: 2023
type: Academic Article
type: Article
type: Document
type: Information Resource

DINC-COVID: A webserver for ensemble docking with flexible SARS-CoV-2 proteins.
PubMed Identifier: 34717233
author list: Hall-Swan S, Devaurs D, Rigo MM, Antunes DA, Kavraki LE, Zanatta G
published in: Computers in biology and medicine
information resource reference: 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.
journal title abbreviation: Comput Biol Med
publication date: 2021-10-15T00:00:00
year: 2021
type: Academic Article
type: Article
type: Document
type: Information Resource

Using parallelized incremental meta-docking can solve the conformational sampling issue when docking large ligands to proteins.
PubMed Identifier: 31488048
author list: Devaurs D, Antunes DA, Hall-Swan S, Mitchell N, Moll M, Liz?e G, Kavraki LE
published in: BMC molecular and cell biology
information resource reference: 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.
journal title abbreviation: BMC Mol Cell Biol
publication date: 2019-09-05T00:00:00
year: 2019
type: Academic Article
type: Article
type: Document
type: Information Resource

Computational and atomistic studies applied to the understanding of the structural and behavioral features of the immune checkpoint HLA-G molecule and gene.
PubMed Identifier: 36710086
author list: Alves CC, Arns T, Oliveira ML, Moreau P, Antunes DA, Castelli EC, Mendes-Junior CT, Giuliatti S, Donadi EA
published in: Human immunology
information resource reference: 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.
journal title abbreviation: Hum Immunol
publication date: 2023-01-27T00:00:00
year: 2023
type: Academic Article
type: Article
type: Document
type: Information Resource

Vestigial-like 1 (VGLL1): An ancient co-transcriptional activator linking wing, placenta, and tumor development.
PubMed Identifier: 37004960
author list: Sonnemann HM, Pazdrak B, Antunes DA, Roszik J, Liz?e G
published in: Biochimica et biophysica acta. Reviews on cancer
information resource reference: 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.
journal title abbreviation: Biochim Biophys Acta Rev Cancer
publication date: 2023-03-31T00:00:00
year: 2023
type: Academic Article
type: Article
type: Document
type: Information Resource

Single-Cell Profiling of CD8+ T Cells in Acute Myeloid Leukemia Reveals a Continuous Spectrum of Differentiation and Clonal Hyperexpansion.
PubMed Identifier: 37163233
author list: 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
published in: Cancer immunology research
information resource reference: 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.
journal title abbreviation: Cancer Immunol Res
publication date: 2023-05-10T00:00:00
year: 2023
type: Academic Article
type: Article
type: Document
type: Information Resource

Individual Epitope-Specific CD8+ T Cell Immune Responses Are Shaped Differently during Chronic Viral Infection.
PubMed Identifier: 37242386
author list: Klein S, Mischke J, Beruldsen F, Prinz I, Antunes DA, Cornberg M, Kraft ARM
published in: Pathogens (Basel, Switzerland)
information resource reference: 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).
journal title abbreviation: Pathogens
publication date: 2023-05-14T00:00:00
year: 2023
type: Academic Article
type: Article
type: Document
type: Information Resource

Markov state modeling reveals alternative unbinding pathways for peptide-MHC complexes.
PubMed Identifier: 33184174
author list: Abella JR, Antunes D, Jackson K, Liz?e G, Clementi C, Kavraki LE
published in: Proceedings of the National Academy of Sciences of the United States of America
information resource reference: 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.
journal title abbreviation: Proc Natl Acad Sci U S A
publication date: 2020-11-12T00:00:00
year: 2020
type: Academic Article
type: Article
type: Document
type: Information Resource

Revealing Unknown Protein Structures Using Computational Conformational Sampling Guided by Experimental Hydrogen-Exchange Data.
PubMed Identifier: 30384411
author list: Devaurs D, Antunes DA, Kavraki LE
published in: International journal of molecular sciences
information resource reference: 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).
journal title abbreviation: Int J Mol Sci
publication date: 2018-10-31T00:00:00
year: 2018
type: Academic Article
type: Article
type: Document
type: Information Resource

HLA-Arena: A Customizable Environment for the Structural Modeling and Analysis of Peptide-HLA Complexes for Cancer Immunotherapy.
PubMed Identifier: 32667823
author list: Antunes DA, Abella JR, Hall-Swan S, Devaurs D, Conev A, Moll M, Liz?e G, Kavraki LE
published in: JCO clinical cancer informatics
information resource reference: 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.
journal title abbreviation: JCO Clin Cancer Inform
publication date: 2020-07-01T00:00:00
year: 2020
type: Academic Article
type: Article
type: Document
type: Information Resource

Interpreting T-Cell Cross-reactivity through Structure: Implications for TCR-Based Cancer Immunotherapy.
PubMed Identifier: 29046675
author list: Antunes DA, Rigo MM, Freitas MV, Mendes MFA, Sinigaglia M, Liz?e G, Kavraki LE, Selin LK, Cornberg M, Vieira GF
published in: Frontiers in immunology
information resource reference: 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.
journal title abbreviation: Front Immunol
publication date: 2017-10-04T00:00:00
year: 2017
type: Academic Article
type: Article
type: Document
type: Information Resource

Computational analysis of complement inhibitor compstatin using molecular dynamics.
PubMed Identifier: 32789582
author list: Devaurs D, Antunes DA, Kavraki LE
published in: Journal of molecular modeling
information resource reference: Devaurs D, Antunes DA, Kavraki LE. Computational analysis of complement inhibitor compstatin using molecular dynamics. J Mol Model. 2020 Aug 12; 26(9):231.
journal title abbreviation: J Mol Model
publication date: 2020-08-12T00:00:00
year: 2020
type: Academic Article
type: Article
type: Document
type: Information Resource

Large-Scale Structure-Based Prediction of Stable Peptide Binding to Class I HLAs Using Random Forests.
PubMed Identifier: 32793224
author list: Abella JR, Antunes DA, Clementi C, Kavraki LE
published in: Frontiers in immunology
information resource reference: 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.
journal title abbreviation: Front Immunol
publication date: 2020-07-22T00:00:00
year: 2020
type: Academic Article
type: Article
type: Document
type: Information Resource

3pHLA-score improves structure-based peptide-HLA binding affinity prediction.
PubMed Identifier: 35750701
author list: Conev A, Devaurs D, Rigo MM, Antunes DA, Kavraki LE
published in: Scientific reports
information resource reference: 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.
journal title abbreviation: Sci Rep
publication date: 2022-06-24T00:00:00
year: 2022
type: Academic Article
type: Article
type: Document
type: Information Resource

SARS-Arena: Sequence and Structure-Guided Selection of Conserved Peptides from SARS-related Coronaviruses for Novel Vaccine Development.
PubMed Identifier: 35903104
author list: Rigo MM, Fasoulis R, Conev A, Hall-Swan S, Antunes DA, Kavraki LE
published in: Frontiers in immunology
information resource reference: 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.
journal title abbreviation: Front Immunol
publication date: 2022-07-12T00:00:00
year: 2022
type: Academic Article
type: Article
type: Document
type: Information Resource

Lessons from molecular modeling human a-L-iduronidase.
PubMed Identifier: 25459762
author list: Figueiredo DF, Antunes DA, Rigo MM, Mendes MF, Silva JP, Mayer FQ, Matte U, Giugliani R, Vieira GF, Sinigaglia M
published in: Journal of molecular graphics & modelling
information resource reference: 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.
journal title abbreviation: J Mol Graph Model
publication date: 2014-10-18T00:00:00
year: 2014
type: Academic Article
type: Article
type: Document
type: Information Resource

DockTope: a Web-based tool for automated pMHC-I modelling.
PubMed Identifier: 26674250
author list: Rigo MM, Antunes DA, Vaz de Freitas M, Fabiano de Almeida Mendes M, Meira L, Sinigaglia M, Vieira GF
published in: Scientific reports
information resource reference: 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.
journal title abbreviation: Sci Rep
publication date: 2015-12-17T00:00:00
year: 2015
type: Academic Article
type: Article
type: Document
type: Information Resource

Frequency, Private Specificity, and Cross-Reactivity of Preexisting Hepatitis C Virus (HCV)-Specific CD8+ T Cells in HCV-Seronegative Individuals: Implications for Vaccine Responses.
PubMed Identifier: 26041301
author list: 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
published in: Journal of virology
information resource reference: 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.
journal title abbreviation: J Virol
publication date: 2015-06-03T00:00:00
year: 2015
type: Academic Article
type: Article
type: Document
type: Information Resource

Improved structural method for T-cell cross-reactivity prediction.
PubMed Identifier: 26141239
author list: Mendes MF, Antunes DA, Rigo MM, Sinigaglia M, Vieira GF
published in: Molecular immunology
information resource reference: 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.
journal title abbreviation: Mol Immunol
publication date: 2015-07-02T00:00:00
year: 2015
type: Academic Article
type: Article
type: Document
type: Information Resource

New insights into the in silico prediction of HIV protease resistance to nelfinavir.
PubMed Identifier: 24498124
author list: Antunes DA, Rigo MM, Sinigaglia M, de Medeiros RM, Junqueira DM, Almeida SE, Vieira GF
published in: PloS one
information resource reference: 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.
journal title abbreviation: PLoS One
publication date: 2014-01-31T00:00:00
year: 2014
type: Academic Article
type: Article
type: Document
type: Information Resource

DINC 2.0: A New Protein-Peptide Docking Webserver Using an Incremental Approach.
PubMed Identifier: 29092940
author list: Antunes DA, Moll M, Devaurs D, Jackson KR, Liz?e G, Kavraki LE
published in: Cancer research
information resource reference: 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.
journal title abbreviation: Cancer Res
publication date: 2017-11-01T00:00:00
year: 2017
type: Academic Article
type: Article
type: Document
type: Information Resource

General Prediction of Peptide-MHC Binding Modes Using Incremental Docking: A Proof of Concept.
PubMed Identifier: 29531253
author list: Antunes DA, Devaurs D, Moll M, Liz?e G, Kavraki LE
published in: Scientific reports
information resource reference: 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.
journal title abbreviation: Sci Rep
publication date: 2018-03-12T00:00:00
year: 2018
type: Academic Article
type: Article
type: Document
type: Information Resource

Coarse-Grained Conformational Sampling of Protein Structure Improves the Fit to Experimental Hydrogen-Exchange Data.
PubMed Identifier: 28344973
author list: Devaurs D, Antunes DA, Papanastasiou M, Moll M, Ricklin D, Lambris JD, Kavraki LE
published in: Frontiers in molecular biosciences
information resource reference: 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.
journal title abbreviation: Front Mol Biosci
publication date: 2017-03-10T00:00:00
year: 2017
type: Academic Article
type: Article
type: Document
type: Information Resource

Computational Modeling of Molecular Structures Guided by Hydrogen-Exchange Data.
PubMed Identifier: 35077179
author list: Devaurs D, Antunes DA, Borysik AJ
published in: Journal of the American Society for Mass Spectrometry
information resource reference: 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.
journal title abbreviation: J Am Soc Mass Spectrom
publication date: 2022-01-25T00:00:00
year: 2022
type: Academic Article
type: Article
type: Document
type: Information Resource

Structure-based Methods for Binding Mode and Binding Affinity Prediction for Peptide-MHC Complexes.
PubMed Identifier: 30582480
author list: Antunes DA, Abella JR, Devaurs D, Rigo MM, Kavraki LE
published in: Current topics in medicinal chemistry
information resource reference: 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.
journal title abbreviation: Curr Top Med Chem
publication date: 2018-01-01T00:00:00
year: 2018
type: Academic Article
type: Article
type: Document
type: Information Resource

APE-Gen: A Fast Method for Generating Ensembles of Bound Peptide-MHC Conformations.
PubMed Identifier: 30832312
author list: Abella JR, Antunes DA, Clementi C, Kavraki LE
published in: Molecules (Basel, Switzerland)
information resource reference: 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).
journal title abbreviation: Molecules
publication date: 2019-03-02T00:00:00
year: 2019
type: Academic Article
type: Article
type: Document
type: Information Resource

Native State of Complement Protein C3d Analysed via Hydrogen Exchange and Conformational Sampling.
PubMed Identifier: 30700993
author list: Devaurs D, Papanastasiou M, Antunes DA, Abella JR, Moll M, Ricklin D, Lambris JD, Kavraki LE
published in: International journal of computational biology and drug design
information resource reference: 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.
journal title abbreviation: Int J Comput Biol Drug Des
publication date: 2018-03-24T00:00:00
year: 2018
type: Academic Article
type: Article
type: Document
type: Information Resource

Strengths and limitations of web servers for the modeling of TCRpMHC complexes.
PubMed Identifier: 39104710
author list: Le HN, de Freitas MV, Antunes DA
published in: Computational and structural biotechnology journal
information resource reference: 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.
journal title abbreviation: Comput Struct Biotechnol J
publication date: 2024-07-01T00:00:00
year: 2024
type: Academic Article
type: Article
type: Document
type: Information Resource

The Role of Vimentin Peptide Citrullination in the Structure and Dynamics of HLA-DRB1 Rheumatoid Arthritis Risk-Associated Alleles.
PubMed Identifier: 39795892
author list: Alves CC, Lewis J, Antunes DA, Donadi EA
published in: International journal of molecular sciences
information resource reference: 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).
journal title abbreviation: Int J Mol Sci
publication date: 2024-12-24T00:00:00
year: 2024
type: Academic Article
type: Article
type: Document
type: Information Resource

Current progress and open challenges for applying deep learning across the biosciences.
PubMed Identifier: 35365602
author list: 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
published in: Nature communications
information resource reference: 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.
journal title abbreviation: Nat Commun
publication date: 2022-04-01T00:00:00
year: 2022
type: Academic Article
type: Article
type: Document
type: Information Resource

Charge-based interactions through peptide position 4 drive diversity of antigen presentation by human leukocyte antigen class I molecules.
PubMed Identifier: 36003074
author list: 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
published in: PNAS nexus
information resource reference: 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.
journal title abbreviation: PNAS Nexus
publication date: 2022-07-27T00:00:00
year: 2022
type: Academic Article
type: Article
type: Document
type: Information Resource

City College, CUNY
type: Organization

Hunter College, CUNY
type: Organization

Jackson State University
type: Organization

University of Hawaii at Manoa
type: Organization

University of Houston
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Peptides
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MeSH semantic group name: Chemicals & Drugs
number of authors: 190
number of publications: 357
uniqueness weight: 0.78753
type: Concept

Proteins
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MeSH semantic group name: Chemicals & Drugs
number of authors: 204
number of publications: 383
uniqueness weight: 0.796849
type: Concept

Receptors, Antigen, T-Cell
MeSH DescriptorUI: D011948
MeSH semantic group name: Chemicals & Drugs
number of authors: 38
number of publications: 66
uniqueness weight: 0.953092
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T-Lymphocytes
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MeSH semantic group name: Anatomy
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number of publications: 378
uniqueness weight: 0.810656
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Histocompatibility Antigens Class I
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MeSH semantic group name: Chemicals & Drugs
number of authors: 19
number of publications: 32
uniqueness weight: 0.974439
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Biology and Biochemistry
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chemistry
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Chemistry and Biochemistry
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Nursing
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Biochemistry
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Leszczynski, Jerzy
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has faculty rank
tag name: prns:hasFacultyRank
type: ObjectProperty

has network
tag name: prns:hasNetwork
type: ObjectProperty

published in
tag name: prns:hasPublicationVenue
type: DatatypeProperty

information resource reference
tag name: prns:informationResourceReference
type: DatatypeProperty

is primary position
tag name: prns:isPrimaryPosition
type: DatatypeProperty

photo
tag name: prns:mainImage
type: ObjectProperty

maximum weight
tag name: prns:maxWeight
type: DatatypeProperty

journal title abbreviation
tag name: prns:medlineTA
type: DatatypeProperty

MeSH DescriptorUI
tag name: prns:meshDescriptorUI
type: DatatypeProperty

MeSH semantic group name
tag name: prns:meshSemanticGroupName
type: DatatypeProperty

minimum weight
tag name: prns:minWeight
type: DatatypeProperty

number of authors
tag name: prns:numberOfAuthors
type: DatatypeProperty

number of connections
tag name: prns:numberOfConnections
type: DatatypeProperty

number of publications
tag name: prns:numberOfPublications
type: DatatypeProperty

Person ID
tag name: prns:personId
type: DatatypeProperty

person in primary position
tag name: prns:personInPrimaryPosition
type: ObjectProperty

position in department
tag name: prns:positionInDepartment
type: ObjectProperty

position in division
tag name: prns:positionInDivision
type: ObjectProperty

predicate node
tag name: prns:predicateNode
type: ObjectProperty

publication date
tag name: prns:publicationDate
type: DatatypeProperty

similar to
tag name: prns:similarTo
type: ObjectProperty

sort order
tag name: prns:sortOrder
type: DatatypeProperty

uniqueness weight
tag name: prns:uniquenessWeight
type: DatatypeProperty

year
tag name: prns:year
type: DatatypeProperty

Academic Article
type: Class

Article
type: Class

Document
type: Class

PubMed Identifier
tag name: bibo:pmid
type: DatatypeProperty

Address
type: Class

address line 1
tag name: vivo:address1
type: DatatypeProperty

city
tag name: vivo:addressCity
type: DatatypeProperty
type: FunctionalProperty

postal code
tag name: vivo:addressPostalCode
type: DatatypeProperty
type: FunctionalProperty

state or province
tag name: vivo:addressState
type: DatatypeProperty
type: FunctionalProperty

selected publications
tag name: vivo:authorInAuthorship
type: ObjectProperty

author rank in publication
tag name: vivo:authorRank
type: DatatypeProperty
type: FunctionalProperty

Authorship
type: Class

Department
type: Class

Division
type: Class

research areas
tag name: vivo:hasResearchArea
type: ObjectProperty

HR job title
tag name: vivo:hrJobTitle
type: DatatypeProperty

Information Resource
type: Class

linked author
tag name: vivo:linkedAuthor
type: ObjectProperty

linked information resource
tag name: vivo:linkedInformationResource
type: ObjectProperty

mailing address
tag name: vivo:mailingAddress
type: ObjectProperty

middle name or initial
tag name: vivo:middleName
type: DatatypeProperty
type: FunctionalProperty

positions
tag name: vivo:personInPosition
type: ObjectProperty

phone
tag name: vivo:phoneNumber
type: DatatypeProperty

Position
type: Class

position in organization
tag name: vivo:positionInOrganization
type: ObjectProperty

preferred title
tag name: vivo:preferredTitle
type: DatatypeProperty
type: FunctionalProperty

predicate
tag name: rdf:predicate
type: ObjectProperty

type
tag name: rdf:type
type: ObjectProperty

label
tag name: rdfs:label
type: DatatypeProperty

Concept
type: Class

Agent
type: Class

first name
tag name: foaf:firstName
type: DatatypeProperty
type: FunctionalProperty

last name
tag name: foaf:lastName
type: DatatypeProperty
type: FunctionalProperty

Organization
type: Class

Person
type: Class