Daisuke Kuroda
Daisuke Kuroda
Verified email at protein.t.u-tokyo.ac.jp - Homepage
TitleCited byYear
Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE)
S Lyskov, FC Chou, SÓ Conchúir, BS Der, K Drew, D Kuroda, J Xu, ...
PloS one 8 (5), 2013
1952013
Computer-aided antibody design
D Kuroda, H Shirai, MP Jacobson, H Nakamura
Protein Engineering Design and Selection 25 (10), 507-522, 2012
1872012
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
1072008
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
942016
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
872016
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, 2017
742017
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
662014
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
622015
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
502009
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
362010
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
322016
Pushing the backbone in protein-protein docking
D Kuroda, JJ Gray
Structure 24 (10), 1821-1829, 2016
292016
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
202017
Extending RosettaDock with water, sugar, and pH for prediction of complex structures and affinities for CAPRI rounds 20–27
KP Kilambi, MS Pacella, J Xu, JW Labonte, JR Porter, P Muthu, K Drew, ...
Proteins: Structure, Function, and Bioinformatics 81 (12), 2201-2209, 2013
202013
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, 413, 2018
182018
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
182015
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
172018
Bridging the gap between single-template and fragment based protein structure modeling using Spanner
M Lis, T Kim, JJ Sarmiento, D Kuroda, HV Dinh, AR Kinjo, K Amada, ...
Immunome research 7 (1), 1, 2011
172011
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), 1-11, 2018
132018
Intramolecular H-bonds govern the recognition of a flexible peptide by an antibody
K Miyanabe, H Akiba, D Kuroda, M Nakakido, O Kusano-Arai, H Iwanari, ...
The Journal of Biochemistry 164 (1), 65-76, 2018
42018
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Articles 1–20