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Results: 1 to 20 of 32

1.

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. eCollection 2014.

PMID:
24625758
[PubMed - in process]
Free PMC Article
2.

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. Epub 2013 Sep 4.

PMID:
23934772
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

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. Epub 2013 Aug 31.

PMID:
23873626
[PubMed - in process]
Free Article
4.

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.

PMID:
23398680
[PubMed]
Free PMC Article
5.

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. Epub 2012 Dec 17.

PMID:
23169174
[PubMed - in process]
Free PMC Article
6.

Functional structural motifs for protein-ligand, protein-protein, and protein-nucleic acid interactions and their connection to supersecondary structures.

Kinjo AR, Nakamura H.

Methods Mol Biol. 2013;932:295-315. doi: 10.1007/978-1-62703-065-6_18.

PMID:
22987360
[PubMed - indexed for MEDLINE]
7.

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. Epub 2011 Nov 30.

PMID:
22369715
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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. Epub 2012 Feb 8.

PMID:
22347478
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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. Epub 2011 Oct 5.

PMID:
21976737
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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.

PMID:
21806842
[PubMed]
Free PMC Article
11.

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. Epub 2011 Jun 22.

PMID:
21723293
[PubMed - indexed for MEDLINE]
Free Article
12.

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.

PMID:
20798081
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*.

Katayama T, Arakawa K, Nakao M, Ono K, Aoki-Kinoshita KF, Yamamoto Y, Yamaguchi A, Kawashima S, Chun HW, Aerts J, Aranda B, Barboza LH, Bonnal RJ, Bruskiewich R, Bryne JC, Fernández JM, Funahashi A, Gordon PM, Goto N, Groscurth A, Gutteridge A, Holland R, Kano Y, Kawas EA, Kerhornou A, Kibukawa E, Kinjo AR, Kuhn M, Lapp H, Lehvaslaiho H, Nakamura H, Nakamura Y, Nishizawa T, Nobata C, Noguchi T, Oinn TM, Okamoto S, Owen S, Pafilis E, Pocock M, Prins P, Ranzinger R, Reisinger F, Salwinski L, Schreiber M, Senger M, Shigemoto Y, Standley DM, Sugawara H, Tashiro T, Trelles O, Vos RA, Wilkinson MD, York W, Zmasek CM, Asai K, Takagi T.

J Biomed Semantics. 2010 Aug 21;1(1):8. doi: 10.1186/2041-1480-1-8.

PMID:
20727200
[PubMed]
Free PMC Article
14.

Geometric similarities of protein-protein interfaces at atomic resolution are only observed within homologous families: an exhaustive structural classification study.

Kinjo AR, Nakamura H.

J Mol Biol. 2010 Jun 11;399(3):526-40. doi: 10.1016/j.jmb.2010.04.028. Epub 2010 Apr 24.

PMID:
20417638
[PubMed - indexed for MEDLINE]
15.

SeSAW: balancing sequence and structural information in protein functional mapping.

Standley DM, Yamashita R, Kinjo AR, Toh H, Nakamura H.

Bioinformatics. 2010 May 1;26(9):1258-9. doi: 10.1093/bioinformatics/btq116. Epub 2010 Mar 17.

PMID:
20299324
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Comprehensive structural classification of ligand-binding motifs in proteins.

Kinjo AR, Nakamura H.

Structure. 2009 Feb 13;17(2):234-46. doi: 10.1016/j.str.2008.11.009.

PMID:
19217394
[PubMed - indexed for MEDLINE]
Free Article
17.

Properties of contact matrices induced by pairwise interactions in proteins.

Miyazawa S, Kinjo AR.

Phys Rev E Stat Nonlin Soft Matter Phys. 2008 May;77(5 Pt 1):051910. Epub 2008 May 14.

PMID:
18643105
[PubMed - indexed for MEDLINE]
18.

Protein structure databases with new web services for structural biology and biomedical research.

Standley DM, Kinjo AR, Kinoshita K, Nakamura H.

Brief Bioinform. 2008 Jul;9(4):276-85. doi: 10.1093/bib/bbn015. Epub 2008 Apr 22. Review.

PMID:
18430752
[PubMed - indexed for MEDLINE]
Free Article
19.

Nature of protein family signatures: insights from singular value analysis of position-specific scoring matrices.

Kinjo AR, Nakamura H.

PLoS One. 2008 Apr 9;3(4):e1963. doi: 10.1371/journal.pone.0001963.

PMID:
18398479
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Wang-Landau molecular dynamics technique to search for low-energy conformational space of proteins.

Nagasima T, Kinjo AR, Mitsui T, Nishikawa K.

Phys Rev E Stat Nonlin Soft Matter Phys. 2007 Jun;75(6 Pt 2):066706. Epub 2007 Jun 27.

PMID:
17677388
[PubMed]

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