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The Protein Data Bank archive as an open data resource.
Berman HM, Kleywegt GJ, Nakamura H, Markley JL. Berman HM, et al. Among authors: nakamura h. J Comput Aided Mol Des. 2014 Oct;28(10):1009-14. doi: 10.1007/s10822-014-9770-y. Epub 2014 Jul 26. J Comput Aided Mol Des. 2014. PMID: 25062767 Free PMC article.
The future of the Protein Data Bank.
Berman HM, Kleywegt GJ, Nakamura H, Markley JL. Berman HM, et al. Among authors: nakamura h. Biopolymers. 2013 Mar;99(3):218-22. doi: 10.1002/bip.22132. Epub 2012 Sep 29. Biopolymers. 2013. PMID: 23023942 Free PMC article. Review.
Remediation of the protein data bank archive.
Henrick K, Feng Z, Bluhm WF, Dimitropoulos D, Doreleijers JF, Dutta S, Flippen-Anderson JL, Ionides J, Kamada C, Krissinel E, Lawson CL, Markley JL, Nakamura H, Newman R, Shimizu Y, Swaminathan J, Velankar S, Ory J, Ulrich EL, Vranken W, Westbrook J, Yamashita R, Yang H, Young J, Yousufuddin M, Berman HM. Henrick K, et al. Among authors: nakamura h. Nucleic Acids Res. 2008 Jan;36(Database issue):D426-33. doi: 10.1093/nar/gkm937. Epub 2007 Dec 11. Nucleic Acids Res. 2008. PMID: 18073189 Free PMC article.
How community has shaped the Protein Data Bank.
Berman HM, Kleywegt GJ, Nakamura H, Markley JL. Berman HM, et al. Among authors: nakamura h. Structure. 2013 Sep 3;21(9):1485-91. doi: 10.1016/j.str.2013.07.010. Structure. 2013. PMID: 24010707 Free PMC article.
Data deposition and annotation at the worldwide protein data bank.
Dutta S, Burkhardt K, Young J, Swaminathan GJ, Matsuura T, Henrick K, Nakamura H, Berman HM. Dutta S, et al. Among authors: nakamura h. Mol Biotechnol. 2009 May;42(1):1-13. doi: 10.1007/s12033-008-9127-7. Epub 2008 Dec 10. Mol Biotechnol. 2009. PMID: 19082769 Review.
Data deposition and annotation at the worldwide protein data bank.
Dutta S, Burkhardt K, Swaminathan GJ, Kosada T, Henrick K, Nakamura H, Berman HM. Dutta S, et al. Among authors: nakamura h. Methods Mol Biol. 2008;426:81-101. doi: 10.1007/978-1-60327-058-8_5. Methods Mol Biol. 2008. PMID: 18542858
Response to On prompt update of literature references in the Protein Data Bank.
Berman HM, Burley SK, Kleywegt GJ, Nakamura H, Markley JL. Berman HM, et al. Among authors: nakamura h. Acta Crystallogr D Biol Crystallogr. 2014 Oct;70(Pt 10):2780. doi: 10.1107/S1399004714020513. Epub 2014 Sep 30. Acta Crystallogr D Biol Crystallogr. 2014. PMID: 25286863 Free PMC article.
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