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Daisuke Kuroda
Daisuke Kuroda
National Institute of Infectious Diseases
Verified email at niid.go.jp - Homepage
Title
Cited by
Cited by
Year
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), e63906, 2013
3142013
Computer-aided antibody design
D Kuroda, H Shirai, MP Jacobson, H Nakamura
Protein Engineering Design and Selection 25 (10), 507-522, 2012
2402012
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
2082020
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
1932017
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
1562016
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
1432016
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
1352008
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
912014
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
902015
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
592009
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
552018
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
522016
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
452010
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
402018
Pushing the backbone in protein-protein docking
D Kuroda, JJ Gray
Structure 24 (10), 1821-1829, 2016
392016
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
382018
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
372015
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
352017
Phospholipid membrane fluidity alters ligand binding activity of a G protein-coupled receptor by shifting the conformational equilibrium
K Yoshida, S Nagatoishi, D Kuroda, N Suzuki, T Murata, K Tsumoto
Biochemistry 58 (6), 504-508, 2019
262019
Exploring designability of electrostatic complementarity at an antigen-antibody interface directed by mutagenesis, biophysical analysis, and molecular dynamics simulations
K Yoshida, D Kuroda, M Kiyoshi, M Nakakido, S Nagatoishi, S Soga, ...
Scientific reports 9 (1), 1-11, 2019
232019
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Articles 1–20