Kuroda Y - Search Results

1

Large-scale all-atom molecular dynamics alanine-scanning of IAPP octapeptides provides insights into the molecular determinants of amyloidogenicity.

Tambi R, Morimoto G, Kosuda S, Taiji M, Kuroda Y. Tambi R, et al. Among authors: kuroda y. Sci Rep. 2019 Feb 21;9(1):2530. doi: 10.1038/s41598-018-38401-w. Sci Rep. 2019. PMID: 30792475 Free PMC article.

2

Experimental identification and theoretical analysis of a thermally stabilized green fluorescent protein variant.

Akiyama S, Suenaga A, Kobayashi T, Kamioka T, Taiji M, Kuroda Y. Akiyama S, et al. Among authors: kuroda y. Biochemistry. 2012 Oct 9;51(40):7974-82. doi: 10.1021/bi300580j. Epub 2012 Sep 27. Biochemistry. 2012. PMID: 22963334

3

All-atom molecular dynamics analysis of multi-peptide systems reproduces peptide solubility in line with experimental observations.

Kuroda Y, Suenaga A, Sato Y, Kosuda S, Taiji M. Kuroda Y, et al. Sci Rep. 2016 Jan 28;6:19479. doi: 10.1038/srep19479. Sci Rep. 2016. PMID: 26817663 Free PMC article.

4

Crystal structures of highly simplified BPTIs provide insights into hydration-driven increase of unfolding enthalpy.

Islam MM, Yohda M, Kidokoro SI, Kuroda Y. Islam MM, et al. Among authors: kuroda y. Sci Rep. 2017 Mar 7;7:41205. doi: 10.1038/srep41205. Sci Rep. 2017. PMID: 28266637 Free PMC article.

5

Solution structure of Gaussia Luciferase with five disulfide bonds and identification of a putative coelenterazine binding cavity by heteronuclear NMR.

Wu N, Kobayashi N, Tsuda K, Unzai S, Saotome T, Kuroda Y, Yamazaki T. Wu N, et al. Among authors: kuroda y. Sci Rep. 2020 Nov 18;10(1):20069. doi: 10.1038/s41598-020-76486-4. Sci Rep. 2020. PMID: 33208800 Free PMC article.

6

Modeling and experimental assessment of a buried Leu-Ile mutation in dengue envelope domain III.

Kulkarni MR, Numoto N, Ito N, Kuroda Y. Kulkarni MR, et al. Among authors: kuroda y. Biochem Biophys Res Commun. 2016 Feb 26;471(1):163-8. doi: 10.1016/j.bbrc.2016.01.159. Epub 2016 Jan 28. Biochem Biophys Res Commun. 2016. PMID: 26826384

7

Fast H-DROP: A thirty times accelerated version of H-DROP for interactive SVM-based prediction of helical domain linkers.

Richa T, Ide S, Suzuki R, Ebina T, Kuroda Y. Richa T, et al. Among authors: kuroda y. J Comput Aided Mol Des. 2017 Feb;31(2):237-244. doi: 10.1007/s10822-016-9999-8. Epub 2016 Dec 27. J Comput Aided Mol Des. 2017. PMID: 28028736

8

Stochastic modelling of the effects of human-mobility restriction and viral infection characteristics on the spread of COVID-19.

Ando S, Matsuzawa Y, Tsurui H, Mizutani T, Hall D, Kuroda Y. Ando S, et al. Among authors: kuroda y. Sci Rep. 2021 Mar 25;11(1):6856. doi: 10.1038/s41598-021-86027-2. Sci Rep. 2021. PMID: 33767233 Free PMC article.

9

Crystal structure of an extensively simplified variant of bovine pancreatic trypsin inhibitor in which over one-third of the residues are alanines.

Islam MM, Sohya S, Noguchi K, Yohda M, Kuroda Y. Islam MM, et al. Among authors: kuroda y. Proc Natl Acad Sci U S A. 2008 Oct 7;105(40):15334-9. doi: 10.1073/pnas.0802699105. Epub 2008 Sep 30. Proc Natl Acad Sci U S A. 2008. PMID: 18829434 Free PMC article.

10

Loop-length-dependent SVM prediction of domain linkers for high-throughput structural proteomics.

Ebina T, Toh H, Kuroda Y. Ebina T, et al. Among authors: kuroda y. Biopolymers. 2009;92(1):1-8. doi: 10.1002/bip.21105. Biopolymers. 2009. PMID: 18844295

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