Kawabata T - Search Results

1

New tools and functions in data-out activities at Protein Data Bank Japan (PDBj).

Kinjo AR, Bekker GJ, Wako H, Endo S, Tsuchiya Y, Sato H, Nishi H, Kinoshita K, Suzuki H, Kawabata T, Yokochi M, Iwata T, Kobayashi N, Fujiwara T, Kurisu G, Nakamura H. Kinjo AR, et al. Among authors: kawabata t. Protein Sci. 2018 Jan;27(1):95-102. doi: 10.1002/pro.3273. Epub 2017 Sep 18. Protein Sci. 2018. PMID: 28815765 Free PMC article.

2

Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data.

Bekker GJ, Yokochi M, Suzuki H, Ikegawa Y, Iwata T, Kudou T, Yura K, Fujiwara T, Kawabata T, Kurisu G. Bekker GJ, et al. Among authors: kawabata t. Protein Sci. 2022 Jan;31(1):173-186. doi: 10.1002/pro.4211. Epub 2021 Oct 27. Protein Sci. 2022. PMID: 34664328 Free PMC article.

3

Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures.

Kinjo AR, Bekker GJ, Suzuki H, Tsuchiya Y, Kawabata T, Ikegawa Y, Nakamura H. Kinjo AR, et al. Among authors: kawabata t. Nucleic Acids Res. 2017 Jan 4;45(D1):D282-D288. doi: 10.1093/nar/gkw962. Epub 2016 Oct 26. Nucleic Acids Res. 2017. PMID: 27789697 Free PMC article.

4

Finding evolutionary relations beyond superfamilies: fold-based superfamilies.

Matsuda K, Nishioka T, Kinoshita K, Kawabata T, Go N. Matsuda K, et al. Among authors: kawabata t. Protein Sci. 2003 Oct;12(10):2239-51. doi: 10.1110/ps.0383603. Protein Sci. 2003. PMID: 14500881 Free PMC article.

5

The Biological Structure Model Archive (BSM-Arc): an archive for in silico models and simulations.

Bekker GJ, Kawabata T, Kurisu G. Bekker GJ, et al. Among authors: kawabata t. Biophys Rev. 2020 Apr;12(2):371-375. doi: 10.1007/s12551-020-00632-5. Epub 2020 Feb 5. Biophys Rev. 2020. PMID: 32026396 Free PMC article. Review.

6

3D flexible alignment using 2D maximum common substructure: dependence of prediction accuracy on target-reference chemical similarity.

Kawabata T, Nakamura H. Kawabata T, et al. J Chem Inf Model. 2014 Jul 28;54(7):1850-63. doi: 10.1021/ci500006d. Epub 2014 Jun 23. J Chem Inf Model. 2014. PMID: 24895842

7

Omokage search: shape similarity search service for biomolecular structures in both the PDB and EMDB.

Suzuki H, Kawabata T, Nakamura H. Suzuki H, et al. Among authors: kawabata t. Bioinformatics. 2016 Feb 15;32(4):619-20. doi: 10.1093/bioinformatics/btv614. Epub 2015 Oct 27. Bioinformatics. 2016. PMID: 26508754 Free PMC article.

8

VaProS: a database-integration approach for protein/genome information retrieval.

Gojobori T, Ikeo K, Katayama Y, Kawabata T, Kinjo AR, Kinoshita K, Kwon Y, Migita O, Mizutani H, Muraoka M, Nagata K, Omori S, Sugawara H, Yamada D, Yura K. Gojobori T, et al. Among authors: kawabata t. J Struct Funct Genomics. 2016 Dec;17(4):69-81. doi: 10.1007/s10969-016-9211-3. Epub 2016 Dec 23. J Struct Funct Genomics. 2016. PMID: 28012137 Free PMC article.

9

LigandBox: A database for 3D structures of chemical compounds.

Kawabata T, Sugihara Y, Fukunishi Y, Nakamura H. Kawabata T, et al. Biophysics (Nagoya-shi). 2013 Aug 7;9:113-21. doi: 10.2142/biophysics.9.113. eCollection 2013. Biophysics (Nagoya-shi). 2013. PMID: 27493549 Free PMC article.

10

Cooperative approach for the protein fold recognition.

Ota M, Kawabata T, Kinjo AR, Nishikawa K. Ota M, et al. Among authors: kawabata t. Proteins. 1999;Suppl 3:126-32. doi: 10.1002/(sici)1097-0134(1999)37:3+<126::aid-prot17>3.3.co;2-#. Proteins. 1999. PMID: 10526361

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