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Items: 15

1.

Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive.

Burley SK, Berman HM, Kleywegt GJ, Markley JL, Nakamura H, Velankar S.

Methods Mol Biol. 2017;1607:627-641. doi: 10.1007/978-1-4939-7000-1_26. Review.

2.

Citing a Data Repository: A Case Study of the Protein Data Bank.

Huang YH, Rose PW, Hsu CN.

PLoS One. 2015 Aug 28;10(8):e0136631. doi: 10.1371/journal.pone.0136631. eCollection 2015.

3.

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.

4.

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.

5.

Implementing an X-ray validation pipeline for the Protein Data Bank.

Gore S, Velankar S, Kleywegt GJ.

Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):478-83. doi: 10.1107/S0907444911050359. Epub 2012 Mar 16.

6.

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.

7.

The Protein Data Bank in Europe (PDBe): bringing structure to biology.

Velankar S, Kleywegt GJ.

Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):324-30. doi: 10.1107/S090744491004117X. Epub 2011 Mar 18.

8.

PCDDB: the Protein Circular Dichroism Data Bank, a repository for circular dichroism spectral and metadata.

Whitmore L, Woollett B, Miles AJ, Klose DP, Janes RW, Wallace BA.

Nucleic Acids Res. 2011 Jan;39(Database issue):D480-6. doi: 10.1093/nar/gkq1026. Epub 2010 Nov 11.

9.

PDBe: Protein Data Bank in Europe.

Velankar S, Alhroub Y, Alili A, Best C, Boutselakis HC, Caboche S, Conroy MJ, Dana JM, van Ginkel G, Golovin A, Gore SP, Gutmanas A, Haslam P, Hirshberg M, John M, Lagerstedt I, Mir S, Newman LE, Oldfield TJ, Penkett CJ, Pineda-Castillo J, Rinaldi L, Sahni G, Sawka G, Sen S, Slowley R, Sousa da Silva AW, Suarez-Uruena A, Swaminathan GJ, Symmons MF, Vranken WF, Wainwright M, Kleywegt GJ.

Nucleic Acids Res. 2011 Jan;39(Database issue):D402-10. doi: 10.1093/nar/gkq985. Epub 2010 Nov 2.

10.

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.

11.

TogoWS: integrated SOAP and REST APIs for interoperable bioinformatics Web services.

Katayama T, Nakao M, Takagi T.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W706-11. doi: 10.1093/nar/gkq386. Epub 2010 May 14.

12.

Fast and automated functional classification with MED-SuMo: an application on purine-binding proteins.

Doppelt-Azeroual O, Delfaud F, Moriaud F, de Brevern AG.

Protein Sci. 2010 Apr;19(4):847-67. doi: 10.1002/pro.364.

13.

The European Bioinformatics Institute's data resources.

Brooksbank C, Cameron G, Thornton J.

Nucleic Acids Res. 2010 Jan;38(Database issue):D17-25. doi: 10.1093/nar/gkp986. Epub 2009 Nov 24.

14.

Analysis of HSP90-related folds with MED-SuMo classification approach.

Doppelt-Azeroual O, Moriaud F, Delfaud F, de Brevern AG.

Drug Des Devel Ther. 2009 Sep 21;3:59-72.

15.

Universal partitioning of the hierarchical fold network of 50-residue segments in proteins.

Ito J, Sonobe Y, Ikeda K, Tomii K, Higo J.

BMC Struct Biol. 2009 May 20;9:34. doi: 10.1186/1472-6807-9-34.

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