| Understanding the challenges of protein flexibility in drug design DA Antunes, D Devaurs, LE Kavraki Expert opinion on drug discovery 10 (12), 1301-1313, 2015 | 135 | 2015 |
| DINC 2.0: a new protein–peptide docking webserver using an incremental approach DA Antunes, M Moll, D Devaurs, KR Jackson, G Lizée, LE Kavraki Cancer research 77 (21), e55-e57, 2017 | 102 | 2017 |
| Current progress and open challenges for applying deep learning across the biosciences N Sapoval, A Aghazadeh, MG Nute, DA Antunes, A Balaji, R Baraniuk, ... Nature Communications 13 (1), 1728, 2022 | 72 | 2022 |
| Interpreting T-cell cross-reactivity through structure: implications for TCR-based cancer immunotherapy DA Antunes, MM Rigo, MV Freitas, MFA Mendes, M Sinigaglia, G Lizée, ... Frontiers in immunology 8, 1210, 2017 | 53 | 2017 |
| Neutralizing antibodies to bovine herpesvirus types 1 (BoHV-1) and 5 (BoHV-5) and its subtypes APM Varela, CL Holz, SP Cibulski, TF Teixeira, DA Antunes, AC Franco, ... Veterinary microbiology 142 (3-4), 254-260, 2010 | 52 | 2010 |
| Structure-based methods for binding mode and binding affinity prediction for peptide-MHC complexes DA Antunes, JR Abella, D Devaurs, MM Rigo, LE Kavraki Current topics in medicinal chemistry 18 (26), 2239-2255, 2018 | 51 | 2018 |
| General prediction of peptide-MHC binding modes using incremental docking: a proof of concept DA Antunes, D Devaurs, M Moll, G Lizée, LE Kavraki Scientific reports 8 (1), 4327, 2018 | 46 | 2018 |
| DockTope: a Web-based tool for automated pMHC-I modelling M Menegatti Rigo, D Amaral Antunes, M Vaz de Freitas, ... Scientific reports 5 (1), 18413, 2015 | 44 | 2015 |
| Structural allele-specific patterns adopted by epitopes in the MHC-I cleft and reconstruction of MHC: peptide complexes to cross-reactivity assessment DA Antunes, GF Vieira, MM Rigo, SP Cibulski, M Sinigaglia, JAB Chies PloS one 5 (4), e10353, 2010 | 32 | 2010 |
| Frequency, Private Specificity, and Cross-Reactivity of Preexisting Hepatitis C Virus (HCV)-Specific CD8+ T Cells in HCV-Seronegative Individuals: Implications for … S Zhang, RK Bakshi, PV Suneetha, P Fytili, DA Antunes, GF Vieira, ... Journal of Virology 89 (16), 8304-8317, 2015 | 31 | 2015 |
| Structural in silico analysis of cross-genotype-reactivity among naturally occurring HCV NS3-1073-variants in the context of HLA-A* 02: 01 allele DA Antunes, MM Rigo, JP Silva, SP Cibulski, M Sinigaglia, JAB Chies, ... Molecular immunology 48 (12-13), 1461-1467, 2011 | 30 | 2011 |
| APE-gen: A fast method for generating ensembles of bound peptide-MHC conformations JR Abella, DA Antunes, C Clementi, LE Kavraki Molecules 24 (5), 881, 2019 | 27 | 2019 |
| New Insights into the In Silico Prediction of HIV Protease Resistance to Nelfinavir DA Antunes, MM Rigo, M Sinigaglia, RM de Medeiros, DM Junqueira, ... PLoS One 9 (1), e87520, 2014 | 25 | 2014 |
| CrossTope: a curate repository of 3D structures of immunogenic peptide: MHC complexes M Sinigaglia, DA Antunes, MM Rigo, JAB Chies, GF Vieira Database 2013, 2013 | 25 | 2013 |
| Using parallelized incremental meta-docking can solve the conformational sampling issue when docking large ligands to proteins D Devaurs, DA Antunes, S Hall-Swan, N Mitchell, M Moll, G Lizée, ... BMC molecular and cell biology 20 (1), 1-15, 2019 | 24 | 2019 |
| Improved structural method for T-cell cross-reactivity prediction MFA Mendes, DA Antunes, MM Rigo, M Sinigaglia, GF Vieira Molecular Immunology 67 (2), 303-310, 2015 | 23 | 2015 |
| Coarse-grained conformational sampling of protein structure improves the fit to experimental hydrogen-exchange data D Devaurs, DA Antunes, M Papanastasiou, M Moll, D Ricklin, JD Lambris, ... Frontiers in molecular biosciences 4, 13, 2017 | 22 | 2017 |
| HLA-arena: A customizable environment for the structural modeling and analysis of peptide-HLA complexes for cancer immunotherapy DA Antunes, JR Abella, S Hall-Swan, D Devaurs, A Conev, M Moll, ... JCO Clinical Cancer Informatics 4, 623-636, 2020 | 19 | 2020 |
| Efficacy of an inactivated, recombinant bovine herpesvirus type 5 (BoHV-5) vaccine FS Campos, D Dezen, DA Antunes, HF Santos, TS Arantes, A Cenci, ... Veterinary microbiology 148 (1), 18-26, 2011 | 17 | 2011 |
| Markov state modeling reveals alternative unbinding pathways for peptide–MHC complexes JR Abella, D Antunes, K Jackson, G Lizée, C Clementi, LE Kavraki Proceedings of the National Academy of Sciences 117 (48), 30610-30618, 2020 | 16 | 2020 |
Lydia E. KavrakiRice UniversityVerified email at rice.edu
