☰

Daisuke Kuroda - Publications

Affiliations: 
2011-2014 Chemical & Biomolecular Engineering Johns Hopkins University, Baltimore, MD 
Tree Info Similar researchers PubMed Report error

26 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Khetan R, Curtis R, Deane CM, Hadsund JT, Kar U, Krawczyk K, Kuroda D, Robinson SA, Sormanni P, Tsumoto K, Warwicker J, Martin ACR. Current advances in biopharmaceutical informatics: guidelines, impact and challenges in the computational developability assessment of antibody therapeutics. Mabs. 14: 2020082. PMID 35104168 DOI: 10.1080/19420862.2021.2020082  0.323
2020 Leman JK, Weitzner BD, Lewis SM, Adolf-Bryfogle J, Alam N, Alford RF, Aprahamian M, Baker D, Barlow KA, Barth P, Basanta B, Bender BJ, Blacklock K, Bonet J, Boyken SE, ... ... Kuroda D, et al. Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nature Methods. PMID 32483333 DOI: 10.1038/S41592-020-0848-2  0.642
2020 Kuroda D, Tsumoto K. Engineering Stability, Viscosity, and Immunogenicity of Antibodies by Computational Design. Journal of Pharmaceutical Sciences. PMID 31958430 DOI: 10.1016/J.Xphs.2020.01.011  0.423
2019 Kondo HX, Kiribayashi R, Kuroda D, Kohda J, Kugimiya A, Nakano Y, Tsumoto K, Takano Y. Effects of a remote mutation from the contact paratope on the structure of CDR-H3 in the anti-HIV neutralizing antibody PG16. Scientific Reports. 9: 19840. PMID 31882602 DOI: 10.1038/S41598-019-56154-Y  0.349
2019 Eguchi A, Nakakido M, Nagatoishi S, Kuroda D, Tsumoto K, Nagamune T, Kawahara M. An epitope-directed antibody affinity maturation system utilizing mammalian cell survival as readout. Biotechnology and Bioengineering. PMID 30883677 DOI: 10.1002/Bit.26965  0.374
2019 Yoshida K, Kuroda D, Kiyoshi M, Nakakido M, Nagatoishi S, Soga S, Shirai H, Tsumoto K. Exploring designability of electrostatic complementarity at an antigen-antibody interface directed by mutagenesis, biophysical analysis, and molecular dynamics simulations. Scientific Reports. 9: 4482. PMID 30872635 DOI: 10.1038/S41598-019-40461-5  0.443
2018 Kuroda D, Tsumoto K. Antibody Affinity Maturation by Computational Design. Methods in Molecular Biology (Clifton, N.J.). 1827: 15-34. PMID 30196490 DOI: 10.1007/978-1-4939-8648-4_2  0.427
2018 Miyanabe K, Akiba H, Kuroda D, Nakakido M, Kusano-Arai O, Iwanari H, Hamakubo T, Caaveiro JMM, Tsumoto K. Intramolecular H-bonds govern the recognition of a flexible peptide by an antibody. Journal of Biochemistry. 164: 65-76. PMID 29924367 DOI: 10.2210/Pdb5Yd4/Pdb  0.34
2018 Jeliazkov JR, Sljoka A, Kuroda D, Tsuchimura N, Katoh N, Tsumoto K, Gray JJ. Repertoire Analysis of Antibody CDR-H3 Loops Suggests Affinity Maturation Does Not Typically Result in Rigidification. Frontiers in Immunology. 9: 413. PMID 29545810 DOI: 10.3389/Fimmu.2018.00413  0.592
2018 Kiyoshi M, Caaveiro JMM, Tada M, Tamura H, Tanaka T, Terao Y, Morante K, Harazono A, Hashii N, Shibata H, Kuroda D, Nagatoishi S, Oe S, Ide T, Tsumoto K, et al. Assessing the Heterogeneity of the Fc-Glycan of a Therapeutic Antibody Using an engineered FcγReceptor IIIa-Immobilized Column. Scientific Reports. 8: 3955. PMID 29500371 DOI: 10.1038/S41598-018-22199-8  0.364
2018 Jeliazkov JR, Slojka A, Kuroda D, Tsutchimura N, Tsumoto K, Katoh N, Gray JJ. Evolution of CDR H3 Flexibility at an Immunomic Scale Biophysical Journal. 114. DOI: 10.1016/J.Bpj.2017.11.1060  0.491
2017 Weitzner BD, Jeliazkov JR, Lyskov S, Marze N, Kuroda D, Frick R, Adolf-Bryfogle J, Biswas N, Dunbrack RL, Gray JJ. Modeling and docking of antibody structures with Rosetta. Nature Protocols. 12: 401-416. PMID 28125104 DOI: 10.1038/Nprot.2016.180  0.757
2016 Kuroda D, Gray JJ. Pushing the Backbone in Protein-Protein Docking. Structure (London, England : 1993). PMID 27568930 DOI: 10.1016/J.Str.2016.06.025  0.556
2016 Kuroda D, Gray JJ. Shape complementarity and hydrogen bond preferences in protein-protein interfaces: Implications for antibody modeling and protein-protein docking. Bioinformatics (Oxford, England). PMID 27153634 DOI: 10.1093/Bioinformatics/Btw197  0.555
2016 Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, ... ... Kuroda D, et al. Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment. Proteins. PMID 27122118 DOI: 10.1002/Prot.25007  0.591
2016 DeKosky BJ, Lungu OI, Park D, Johnson EL, Charab W, Chrysostomou C, Kuroda D, Ellington AD, Ippolito GC, Gray JJ, Georgiou G. Large-scale sequence and structural comparisons of human naive and antigen-experienced antibody repertoires. Proceedings of the National Academy of Sciences of the United States of America. PMID 27114511 DOI: 10.1073/Pnas.1525510113  0.562
2014 Weitzner BD, Kuroda D, Marze N, Xu J, Gray JJ. Blind prediction performance of RosettaAntibody 3.0: grafting, relaxation, kinematic loop modeling, and full CDR optimization. Proteins. 82: 1611-23. PMID 24519881 DOI: 10.1002/Prot.24534  0.759
2013 Kilambi KP, Pacella MS, Xu J, Labonte JW, Porter JR, Muthu P, Drew K, Kuroda D, Schueler-Furman O, Bonneau R, Gray JJ. Extending RosettaDock with water, sugar, and pH for prediction of complex structures and affinities for CAPRI rounds 20-27. Proteins. 81: 2201-9. PMID 24123494 DOI: 10.1002/Prot.24425  0.698
2013 Lyskov S, Chou FC, Conchúir SÓ, Der BS, Drew K, Kuroda D, Xu J, Weitzner BD, Renfrew PD, Sripakdeevong P, Borgo B, Havranek JJ, Kuhlman B, Kortemme T, Bonneau R, et al. Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE). Plos One. 8: e63906. PMID 23717507 DOI: 10.1371/Journal.Pone.0063906  0.752
2012 Kuroda D, Shirai H, Jacobson MP, Nakamura H. Computer-aided antibody design. Protein Engineering, Design & Selection : Peds. 25: 507-21. PMID 22661385 DOI: 10.1093/Protein/Gzs024  0.491
2010 Soga S, Kuroda D, Shirai H, Kobori M, Hirayama N. Use of amino acid composition to predict epitope residues of individual antibodies. Protein Engineering, Design & Selection : Peds. 23: 441-8. PMID 20304974 DOI: 10.1093/Protein/Gzq014  0.421
2009 Kuroda D, Shirai H, Kobori M, Nakamura H. Systematic classification of CDR-L3 in antibodies: implications of the light chain subtypes and the VL-VH interface. Proteins. 75: 139-46. PMID 18798566 DOI: 10.1002/Prot.22230  0.42
2008 Kuroda D, Shirai H, Kobori M, Nakamura H. Structural classification of CDR-H3 revisited: a lesson in antibody modeling. Proteins. 73: 608-20. PMID 18473362 DOI: 10.1002/Prot.22087  0.412
2008 Kuroda D, Shirai H, Kobori M, Nakamura H. H3-Rules, Progress Report 2007 Journal of Proteomics & Bioinformatics. 189-190. DOI: 10.4172/Jpb.S1000140  0.421
2008 Kuroda D, Shirai H, Kobori M, Nakamura H. Relationship between sequence and structure of CDR-H3 in antibodies Acta Crystallographica Section a Foundations of Crystallography. 64: C228-C228. DOI: 10.1107/S0108767308092684  0.352
2007 Kuroda D, Shirai H, Nakamura H. 1P270 New classification of the structures of antibody CDR-H3(Genome,Poster Presentations) Seibutsu Butsuri. 47: S91. DOI: 10.2142/Biophys.47.S91_1  0.32
Show low-probability matches.