| Macromolecular modeling and design in Rosetta: recent methods and frameworks JK Leman, BD Weitzner, SM Lewis, J Adolf-Bryfogle, N Alam, RF Alford, ... Nature methods 17 (7), 665-680, 2020 | 560 | 2020 |
| Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE) S Lyskov, FC Chou, SO Conchuir, BS Der, K Drew, D Kuroda, J Xu, ... PloS one 8 (5), e63906, 2013 | 394 | 2013 |
| Computer-aided antibody design D Kuroda, H Shirai, MP Jacobson, H Nakamura Protein Engineering Design and Selection 25 (10), 507-522, 2012 | 287 | 2012 |
| Modeling and docking of antibody structures with Rosetta BD Weitzner, JR Jeliazkov, S Lyskov, N Marze, D Kuroda, R Frick, ... Nature protocols 12 (2), 401-416, 2017 | 262 | 2017 |
| Large-scale sequence and structural comparisons of human naive and antigen-experienced antibody repertoires BJ DeKosky, OI Lungu, D Park, EL Johnson, W Charab, C Chrysostomou, ... Proceedings of the National Academy of Sciences 113 (19), E2636-E2645, 2016 | 202 | 2016 |
| Prediction of homoprotein and heteroprotein complexes by protein docking and template‐based modeling: a CASP‐CAPRI experiment MF Lensink, S Velankar, A Kryshtafovych, SY Huang, ... Proteins: Structure, Function, and Bioinformatics 84, 323-348, 2016 | 164 | 2016 |
| Structural classification of CDR‐H3 revisited: a lesson in antibody modeling D Kuroda, H Shirai, M Kobori, H Nakamura Proteins: Structure, Function, and Bioinformatics 73 (3), 608-620, 2008 | 143 | 2008 |
| Design and synthesis of non-peptide, selective orexin receptor 2 agonists T Nagahara, T Saitoh, N Kutsumura, Y Irukayama-Tomobe, Y Ogawa, ... Journal of medicinal chemistry 58 (20), 7931-7937, 2015 | 124 | 2015 |
| Blind prediction performance of RosettaAntibody 3.0: Grafting, relaxation, kinematic loop modeling, and full CDR optimization BD Weitzner, D Kuroda, N Marze, J Xu, JJ Gray Proteins: Structure, Function, and Bioinformatics 82 (8), 1611–1623, 2014 | 103 | 2014 |
| Shape complementarity and hydrogen bond preferences in protein–protein interfaces: implications for antibody modeling and protein–protein docking D Kuroda, JJ Gray Bioinformatics 32 (16), 2451-2456, 2016 | 79 | 2016 |
| Structures of the prefusion form of measles virus fusion protein in complex with inhibitors T Hashiguchi, Y Fukuda, R Matsuoka, D Kuroda, M Kubota, Y Shirogane, ... Proceedings of the National Academy of Sciences 115 (10), 2496-2501, 2018 | 70 | 2018 |
| Systematic classification of CDR‐L3 in antibodies: Implications of the light chain subtypes and the VL–VH interface D Kuroda, H Shirai, M Kobori, H Nakamura Proteins: Structure, Function, and Bioinformatics 75 (1), 139-146, 2009 | 70 | 2009 |
| Assessing the heterogeneity of the Fc-glycan of a therapeutic antibody using an engineered FcγReceptor IIIa-immobilized column M Kiyoshi, JMM Caaveiro, M Tada, H Tamura, T Tanaka, Y Terao, ... Scientific reports 8 (1), 3955, 2018 | 65 | 2018 |
| Use of amino acid composition to predict epitope residues of individual antibodies S Soga, D Kuroda, H Shirai, M Kobori, N Hirayama Protein Engineering, Design & Selection 23 (6), 441-448, 2010 | 54 | 2010 |
| Pushing the backbone in protein-protein docking D Kuroda, JJ Gray Structure 24 (10), 1821-1829, 2016 | 53 | 2016 |
| Structural insights into the reaction mechanism of S-adenosyl-L-homocysteine hydrolase. Y Kusakabe, M Ishihara, T Umeda, D Kuroda, M Nakanishi, Y Kitade, ... Scientific reports 5, 16641-16641, 2015 | 52 | 2015 |
| Repertoire analysis of antibody CDR-H3 loops suggests affinity maturation does not typically result in rigidification JR Jeliazkov, A Sljoka, D Kuroda, N Tsuchimura, N Katoh, K Tsumoto, ... Frontiers in immunology 9, 338525, 2018 | 50 | 2018 |
| Engineering stability, viscosity, and immunogenicity of antibodies by computational design D Kuroda, K Tsumoto Journal of Pharmaceutical Sciences 109 (5), 1631-1651, 2020 | 49 | 2020 |
| Current advances in biopharmaceutical informatics: guidelines, impact and challenges in the computational developability assessment of antibody therapeutics R Khetan, R Curtis, CM Deane, JT Hadsund, U Kar, K Krawczyk, ... Mabs 14 (1), 2020082, 2022 | 42 | 2022 |
| Design and synthesis of potent and highly selective orexin 1 receptor antagonists with a morphinan skeleton and their pharmacologies H Nagase, N Yamamoto, M Yata, S Ohrui, T Okada, T Saitoh, ... Journal of Medicinal Chemistry 60 (3), 1018-1040, 2017 | 42 | 2017 |
