Format
Sort by
Items per page

Send to

Choose Destination

Links from PubMed

Items: 1 to 20 of 123

1.

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.

Nucleic Acids Res. 2008 Jan;36(Database issue):D426-33. Epub 2007 Dec 11.

2.

The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data.

Berman H, Henrick K, Nakamura H, Markley JL.

Nucleic Acids Res. 2007 Jan;35(Database issue):D301-3. Epub 2006 Nov 16.

3.

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.

PMID:
28573592
4.

E-MSD: improving data deposition and structure quality.

Tagari M, Tate J, Swaminathan GJ, Newman R, Naim A, Vranken W, Kapopoulou A, Hussain A, Fillon J, Henrick K, Velankar S.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D287-90.

5.

The future of the Protein Data Bank.

Berman HM, Kleywegt GJ, Nakamura H, Markley JL.

Biopolymers. 2013 Mar;99(3):218-22. doi: 10.1002/bip.22132. Epub 2012 Sep 29. Review.

6.

The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank.

Westbrook JD, Shao C, Feng Z, Zhuravleva M, Velankar S, Young J.

Bioinformatics. 2015 Apr 15;31(8):1274-8. doi: 10.1093/bioinformatics/btu789. Epub 2014 Dec 2.

7.

OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive.

Young JY, Westbrook JD, Feng Z, Sala R, Peisach E, Oldfield TJ, Sen S, Gutmanas A, Armstrong DR, Berrisford JM, Chen L, Chen M, Di Costanzo L, Dimitropoulos D, Gao G, Ghosh S, Gore S, Guranovic V, Hendrickx PM, Hudson BP, Igarashi R, Ikegawa Y, Kobayashi N, Lawson CL, Liang Y, Mading S, Mak L, Mir MS, Mukhopadhyay A, Patwardhan A, Persikova I, Rinaldi L, Sanz-Garcia E, Sekharan MR, Shao C, Swaminathan GJ, Tan L, Ulrich EL, van Ginkel G, Yamashita R, Yang H, Zhuravleva MA, Quesada M, Kleywegt GJ, Berman HM, Markley JL, Nakamura H, Velankar S, Burley SK.

Structure. 2017 Mar 7;25(3):536-545. doi: 10.1016/j.str.2017.01.004. Epub 2017 Feb 9.

PMID:
28190782
8.

PDBe: Protein Data Bank in Europe.

Gutmanas A, Alhroub Y, Battle GM, Berrisford JM, Bochet E, Conroy MJ, Dana JM, Fernandez Montecelo MA, van Ginkel G, Gore SP, Haslam P, Hatherley R, Hendrickx PM, Hirshberg M, Lagerstedt I, Mir S, Mukhopadhyay A, Oldfield TJ, Patwardhan A, Rinaldi L, Sahni G, Sanz-García E, Sen S, Slowley RA, Velankar S, Wainwright ME, Kleywegt GJ.

Nucleic Acids Res. 2014 Jan;42(Database issue):D285-91. doi: 10.1093/nar/gkt1180. Epub 2013 Nov 27.

9.

BioMagResBank.

Ulrich EL, Akutsu H, Doreleijers JF, Harano Y, Ioannidis YE, Lin J, Livny M, Mading S, Maziuk D, Miller Z, Nakatani E, Schulte CF, Tolmie DE, Kent Wenger R, Yao H, Markley JL.

Nucleic Acids Res. 2008 Jan;36(Database issue):D402-8. Epub 2007 Nov 4.

10.

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.

11.

The Protein Data Bank: unifying the archive.

Westbrook J, Feng Z, Jain S, Bhat TN, Thanki N, Ravichandran V, Gilliland GL, Bluhm W, Weissig H, Greer DS, Bourne PE, Berman HM.

Nucleic Acids Res. 2002 Jan 1;30(1):245-8.

12.

Using MSDchem to search the PDB ligand dictionary.

Dimitropoulos D, Ionides J, Henrick K.

Curr Protoc Bioinformatics. 2006 Oct;Chapter 14:Unit14.3. doi: 10.1002/0471250953.bi1403s15.

PMID:
18428761
13.

Multivariate Analyses of Quality Metrics for Crystal Structures in the PDB Archive.

Shao C, Yang H, Westbrook JD, Young JY, Zardecki C, Burley SK.

Structure. 2017 Mar 7;25(3):458-468. doi: 10.1016/j.str.2017.01.013. Epub 2017 Feb 16.

PMID:
28216043
14.

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. 2017 Jan 4;45(D1):D282-D288. doi: 10.1093/nar/gkw962. Epub 2016 Oct 26.

15.

BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions.

Markley JL, Ulrich EL, Berman HM, Henrick K, Nakamura H, Akutsu H.

J Biomol NMR. 2008 Mar;40(3):153-5. doi: 10.1007/s10858-008-9221-y. Epub 2008 Feb 21.

16.

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.

17.

PDBe: Protein Data Bank in Europe.

Velankar S, Alhroub Y, Best C, Caboche S, Conroy MJ, Dana JM, Fernandez Montecelo MA, van Ginkel G, Golovin A, Gore SP, Gutmanas A, Haslam P, Hendrickx PM, Heuson E, Hirshberg M, John M, Lagerstedt I, Mir S, Newman LE, Oldfield TJ, Patwardhan A, Rinaldi L, Sahni G, Sanz-García E, Sen S, Slowley R, Suarez-Uruena A, Swaminathan GJ, Symmons MF, Vranken WF, Wainwright M, Kleywegt GJ.

Nucleic Acids Res. 2012 Jan;40(Database issue):D445-52. doi: 10.1093/nar/gkr998. Epub 2011 Nov 21.

18.

Chemical annotation of small and peptide-like molecules at the Protein Data Bank.

Young JY, Feng Z, Dimitropoulos D, Sala R, Westbrook J, Zhuravleva M, Shao C, Quesada M, Peisach E, Berman HM.

Database (Oxford). 2013 Nov 29;2013:bat079. doi: 10.1093/database/bat079. Print 2013.

19.

How precise are reported protein coordinate data?

Konagurthu AS, Allison L, Abramson D, Stuckey PJ, Lesk AM.

Acta Crystallogr D Biol Crystallogr. 2014 Mar;70(Pt 3):904-6. doi: 10.1107/S1399004713031787. Epub 2014 Feb 27.

PMID:
24598758
20.

NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB.

Doreleijers JF, Vranken WF, Schulte C, Markley JL, Ulrich EL, Vriend G, Vuister GW.

Nucleic Acids Res. 2012 Jan;40(Database issue):D519-24. doi: 10.1093/nar/gkr1134. Epub 2011 Dec 1.

Supplemental Content

Support Center