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Items: 1 to 20 of 43

1.

Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins.

Yokochi M, Kobayashi N, Ulrich EL, Kinjo AR, Iwata T, Ioannidis YE, Livny M, Markley JL, Nakamura H, Kojima C, Fujiwara T.

J Biomed Semantics. 2016 May 5;7(1):16.

PMID:
27927232
2.
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.

Nucleic Acids Res. 2016 Oct 26. pii: gkw962. [Epub ahead of print]

4.

Molmil: a molecular viewer for the PDB and beyond.

Bekker GJ, Nakamura H, Kinjo AR.

J Cheminform. 2016 Aug 26;8(1):42. doi: 10.1186/s13321-016-0155-1.

5.

Implementation of linked data in the life sciences at BioHackathon 2011.

Aoki-Kinoshita KF, Kinjo AR, Morita M, Igarashi Y, Chen YA, Shigemoto Y, Fujisawa T, Akune Y, Katoda T, Kokubu A, Mori T, Nakao M, Kawashima S, Okamoto S, Katayama T, Ogishima S.

J Biomed Semantics. 2015 Jan 7;6:3. doi: 10.1186/2041-1480-6-3. Review.

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7.

Specific non-local interactions are not necessary for recovering native protein dynamics.

Dasgupta B, Kasahara K, Kamiya N, Nakamura H, Kinjo AR.

PLoS One. 2014 Mar 13;9(3):e91347. doi: 10.1371/journal.pone.0091347.

8.

Cooperation between phenotypic plasticity and genetic mutations can account for the cumulative selection in evolution.

Nishikawa K, Kinjo AR.

Biophysics (Nagoya-shi). 2014 Dec 17;10:99-108. doi: 10.2142/biophysics.10.99.

9.

Exhaustive comparison and classification of ligand-binding surfaces in proteins.

Murakami Y, Kinoshita K, Kinjo AR, Nakamura H.

Protein Sci. 2013 Oct;22(10):1379-91. doi: 10.1002/pro.2329.

10.

Rigid-body motions of interacting proteins dominate multispecific binding of ubiquitin in a shape-dependent manner.

Dasgupta B, Nakamura H, Kinjo AR.

Proteins. 2014 Jan;82(1):77-89. doi: 10.1002/prot.24371.

11.

The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies.

Katayama T, Wilkinson MD, Micklem G, Kawashima S, Yamaguchi A, Nakao M, Yamamoto Y, Okamoto S, Oouchida K, Chun HW, Aerts J, Afzal H, Antezana E, Arakawa K, Aranda B, Belleau F, Bolleman J, Bonnal RJ, Chapman B, Cock PJ, Eriksson T, Gordon PM, Goto N, Hayashi K, Horn H, Ishiwata R, Kaminuma E, Kasprzyk A, Kawaji H, Kido N, Kim YJ, Kinjo AR, Konishi F, Kwon KH, Labarga A, Lamprecht AL, Lin Y, Lindenbaum P, McCarthy L, Morita H, Murakami K, Nagao K, Nishida K, Nishimura K, Nishizawa T, Ogishima S, Ono K, Oshita K, Park KJ, Prins P, Saito TL, Samwald M, Satagopam VP, Shigemoto Y, Smith R, Splendiani A, Sugawara H, Taylor J, Vos RA, Withers D, Yamasaki C, Zmasek CM, Kawamoto S, Okubo K, Asai K, Takagi T.

J Biomed Semantics. 2013 Feb 11;4(1):6. doi: 10.1186/2041-1480-4-6.

12.

Counterbalance of ligand- and self-coupled motions characterizes multispecificity of ubiquitin.

Dasgupta B, Nakamura H, Kinjo AR.

Protein Sci. 2013 Feb;22(2):168-78. doi: 10.1002/pro.2195.

13.
14.

Functional characterization of protein domains common to animal viruses and mouse.

Kinjo AR, Kumagai Y, Dinh H, Takeuchi O, Standley DM.

BMC Genomics. 2011 Nov 30;12 Suppl 3:S21. doi: 10.1186/1471-2164-12-S3-S21.

15.

Composite structural motifs of binding sites for delineating biological functions of proteins.

Kinjo AR, Nakamura H.

PLoS One. 2012;7(2):e31437. doi: 10.1371/journal.pone.0031437.

16.

GIRAF: a method for fast search and flexible alignment of ligand binding interfaces in proteins at atomic resolution.

Kinjo AR, Nakamura H.

Biophysics (Nagoya-shi). 2012 May 31;8:79-94. doi: 10.2142/biophysics.8.79.

17.

Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format.

Kinjo AR, Suzuki H, Yamashita R, Ikegawa Y, Kudou T, Igarashi R, Kengaku Y, Cho H, Standley DM, Nakagawa A, Nakamura H.

Nucleic Acids Res. 2012 Jan;40(Database issue):D453-60. doi: 10.1093/nar/gkr811.

18.

The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications.

Katayama T, Wilkinson MD, Vos R, Kawashima T, Kawashima S, Nakao M, Yamamoto Y, Chun HW, Yamaguchi A, Kawano S, Aerts J, Aoki-Kinoshita KF, Arakawa K, Aranda B, Bonnal RJ, Fernández JM, Fujisawa T, Gordon PM, Goto N, Haider S, Harris T, Hatakeyama T, Ho I, Itoh M, Kasprzyk A, Kido N, Kim YJ, Kinjo AR, Konishi F, Kovarskaya Y, von Kuster G, Labarga A, Limviphuvadh V, McCarthy L, Nakamura Y, Nam Y, Nishida K, Nishimura K, Nishizawa T, Ogishima S, Oinn T, Okamoto S, Okuda S, Ono K, Oshita K, Park KJ, Putnam N, Senger M, Severin J, Shigemoto Y, Sugawara H, Taylor J, Trelles O, Yamasaki C, Yamashita R, Satoh N, Takagi T.

J Biomed Semantics. 2011 Aug 2;2:4. doi: 10.1186/2041-1480-2-4.

19.

Distinct roles of overlapping and non-overlapping regions of hub protein interfaces in recognition of multiple partners.

Dasgupta B, Nakamura H, Kinjo AR.

J Mol Biol. 2011 Aug 19;411(3):713-27. doi: 10.1016/j.jmb.2011.06.027.

20.

PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan.

Kinjo AR, Yamashita R, Nakamura H.

Database (Oxford). 2010 Aug 25;2010:baq021. doi: 10.1093/database/baq021.

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