Kuroda D - Search Results

1

Kuroda D, Shirai H, Jacobson MP, Nakamura H. Kuroda D, et al. Protein Eng Des Sel. 2012 Oct;25(10):507-21. doi: 10.1093/protein/gzs024. Epub 2012 Jun 2. Protein Eng Des Sel. 2012. PMID: 22661385 Free PMC article. Review.

2

Structural classification of CDR-H3 revisited: a lesson in antibody modeling.

Kuroda D, Shirai H, Kobori M, Nakamura H. Kuroda D, et al. Proteins. 2008 Nov 15;73(3):608-20. doi: 10.1002/prot.22087. Proteins. 2008. PMID: 18473362

3

Systematic classification of CDR-L3 in antibodies: implications of the light chain subtypes and the VL-VH interface.

Kuroda D, Shirai H, Kobori M, Nakamura H. Kuroda D, et al. Proteins. 2009 Apr;75(1):139-46. doi: 10.1002/prot.22230. Proteins. 2009. PMID: 18798566

4

Use of amino acid composition to predict epitope residues of individual antibodies.

Soga S, Kuroda D, Shirai H, Kobori M, Hirayama N. Soga S, et al. Among authors: kuroda d. Protein Eng Des Sel. 2010 Jun;23(6):441-8. doi: 10.1093/protein/gzq014. Epub 2010 Mar 19. Protein Eng Des Sel. 2010. PMID: 20304974

5

Antibody Affinity Maturation by Computational Design.

Kuroda D, Tsumoto K. Kuroda D, et al. Methods Mol Biol. 2018;1827:15-34. doi: 10.1007/978-1-4939-8648-4_2. Methods Mol Biol. 2018. PMID: 30196490

6

Exploring designability of electrostatic complementarity at an antigen-antibody interface directed by mutagenesis, biophysical analysis, and molecular dynamics simulations.

Yoshida K, Kuroda D, Kiyoshi M, Nakakido M, Nagatoishi S, Soga S, Shirai H, Tsumoto K. Yoshida K, et al. Among authors: kuroda d. Sci Rep. 2019 Mar 14;9(1):4482. doi: 10.1038/s41598-019-40461-5. Sci Rep. 2019. PMID: 30872635 Free PMC article.

7

Effects of a remote mutation from the contact paratope on the structure of CDR-H3 in the anti-HIV neutralizing antibody PG16.

Kondo HX, Kiribayashi R, Kuroda D, Kohda J, Kugimiya A, Nakano Y, Tsumoto K, Takano Y. Kondo HX, et al. Among authors: kuroda d. Sci Rep. 2019 Dec 27;9(1):19840. doi: 10.1038/s41598-019-56154-y. Sci Rep. 2019. PMID: 31882602 Free PMC article.

8

Engineering Stability, Viscosity, and Immunogenicity of Antibodies by Computational Design.

Kuroda D, Tsumoto K. Kuroda D, et al. J Pharm Sci. 2020 May;109(5):1631-1651. doi: 10.1016/j.xphs.2020.01.011. Epub 2020 Jan 18. J Pharm Sci. 2020. PMID: 31958430 Free article. Review.

9

Structural basis for antigen recognition by methylated lysine-specific antibodies.

Ishii M, Nakakido M, Caaveiro JMM, Kuroda D, Okumura CJ, Maruyama T, Entzminger K, Tsumoto K. Ishii M, et al. Among authors: kuroda d. J Biol Chem. 2021 Jan-Jun;296:100176. doi: 10.1074/jbc.RA120.015996. Epub 2020 Dec 17. J Biol Chem. 2021. PMID: 33303630 Free PMC article.

10

Modeling and docking of antibody structures with Rosetta.

Weitzner BD, Jeliazkov JR, Lyskov S, Marze N, Kuroda D, Frick R, Adolf-Bryfogle J, Biswas N, Dunbrack RL Jr, Gray JJ. Weitzner BD, et al. Among authors: kuroda d. Nat Protoc. 2017 Feb;12(2):401-416. doi: 10.1038/nprot.2016.180. Epub 2017 Jan 26. Nat Protoc. 2017. PMID: 28125104 Free PMC article.

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