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Items: 1 to 20 of 99

1.

Report of the wwPDB Small-Angle Scattering Task Force: data requirements for biomolecular modeling and the PDB.

Trewhella J, Hendrickson WA, Kleywegt GJ, Sali A, Sato M, Schwede T, Svergun DI, Tainer JA, Westbrook J, Berman HM.

Structure. 2013 Jun 4;21(6):875-81. doi: 10.1016/j.str.2013.04.020. Review.

2.

SASBDB, a repository for biological small-angle scattering data.

Valentini E, Kikhney AG, Previtali G, Jeffries CM, Svergun DI.

Nucleic Acids Res. 2015 Jan;43(Database issue):D357-63. doi: 10.1093/nar/gku1047. Epub 2014 Oct 28.

3.

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.

4.

The dynamic duo: combining NMR and small angle scattering in structural biology.

Hennig J, Sattler M.

Protein Sci. 2014 Jun;23(6):669-82. doi: 10.1002/pro.2467. Epub 2014 Apr 17. Review.

5.

Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop.

Sali A, Berman HM, Schwede T, Trewhella J, Kleywegt G, Burley SK, Markley J, Nakamura H, Adams P, Bonvin AM, Chiu W, Peraro MD, Di Maio F, Ferrin TE, Grünewald K, Gutmanas A, Henderson R, Hummer G, Iwasaki K, Johnson G, Lawson CL, Meiler J, Marti-Renom MA, Montelione GT, Nilges M, Nussinov R, Patwardhan A, Rappsilber J, Read RJ, Saibil H, Schröder GF, Schwieters CD, Seidel CA, Svergun D, Topf M, Ulrich EL, Velankar S, Westbrook JD.

Structure. 2015 Jul 7;23(7):1156-67. doi: 10.1016/j.str.2015.05.013. Epub 2015 Jun 18.

6.

Extension of the sasCIF format and its applications for data processing and deposition.

Kachala M, Westbrook J, Svergun D.

J Appl Crystallogr. 2016 Feb 1;49(Pt 1):302-310. eCollection 2016 Feb 1.

7.

A structure refinement protocol combining NMR residual dipolar couplings and small angle scattering restraints.

Gabel F, Simon B, Nilges M, Petoukhov M, Svergun D, Sattler M.

J Biomol NMR. 2008 Aug;41(4):199-208. doi: 10.1007/s10858-008-9258-y. Epub 2008 Aug 1.

PMID:
18670889
8.

Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop.

Adams PD, Aertgeerts K, Bauer C, Bell JA, Berman HM, Bhat TN, Blaney JM, Bolton E, Bricogne G, Brown D, Burley SK, Case DA, Clark KL, Darden T, Emsley P, Feher VA, Feng Z, Groom CR, Harris SF, Hendle J, Holder T, Joachimiak A, Kleywegt GJ, Krojer T, Marcotrigiano J, Mark AE, Markley JL, Miller M, Minor W, Montelione GT, Murshudov G, Nakagawa A, Nakamura H, Nicholls A, Nicklaus M, Nolte RT, Padyana AK, Peishoff CE, Pieniazek S, Read RJ, Shao C, Sheriff S, Smart O, Soisson S, Spurlino J, Stouch T, Svobodova R, Tempel W, Terwilliger TC, Tronrud D, Velankar S, Ward SC, Warren GL, Westbrook JD, Williams P, Yang H, Young J.

Structure. 2016 Apr 5;24(4):502-8. doi: 10.1016/j.str.2016.02.017.

PMID:
27050687
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.

10.

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.

11.

Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS).

Perkins SJ, Wright DW, Zhang H, Brookes EH, Chen J, Irving TC, Krueger S, Barlow DJ, Edler KJ, Scott DJ, Terrill NJ, King SM, Butler PD, Curtis JE.

J Appl Crystallogr. 2016 Oct 14;49(Pt 6):1861-1875. eCollection 2016 Oct 14.

12.

Small angle neutron and X-ray scattering in structural biology: recent examples from the literature.

Neylon C.

Eur Biophys J. 2008 Jun;37(5):531-41. doi: 10.1007/s00249-008-0259-2. Epub 2008 Jan 23. Review.

PMID:
18214466
13.

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.

14.

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.

15.

Effect of interdomain dynamics on the structure determination of modular proteins by small-angle scattering.

Bernadó P.

Eur Biophys J. 2010 Apr;39(5):769-80. doi: 10.1007/s00249-009-0549-3. Epub 2009 Oct 21.

PMID:
19844700
16.

A new generation of crystallographic validation tools for the protein data bank.

Read RJ, Adams PD, Arendall WB 3rd, Brunger AT, Emsley P, Joosten RP, Kleywegt GJ, Krissinel EB, Lütteke T, Otwinowski Z, Perrakis A, Richardson JS, Sheffler WH, Smith JL, Tickle IJ, Vriend G, Zwart PH.

Structure. 2011 Oct 12;19(10):1395-412. doi: 10.1016/j.str.2011.08.006.

17.

Recommendations of the wwPDB NMR Validation Task Force.

Montelione GT, Nilges M, Bax A, Güntert P, Herrmann T, Richardson JS, Schwieters CD, Vranken WF, Vuister GW, Wishart DS, Berman HM, Kleywegt GJ, Markley JL.

Structure. 2013 Sep 3;21(9):1563-70. doi: 10.1016/j.str.2013.07.021.

18.

A simple procedure to evaluate the efficiency of bio-macromolecular rigid-body refinement by small-angle scattering.

Gabel F.

Eur Biophys J. 2012 Jan;41(1):1-11. doi: 10.1007/s00249-011-0751-y. Epub 2011 Sep 24.

PMID:
21947509
19.

Whaddaya Know: A Guide to Uncertainty and Subjectivity in Structural Biology.

Mackay JP, Landsberg MJ, Whitten AE, Bond CS.

Trends Biochem Sci. 2017 Feb;42(2):155-167. doi: 10.1016/j.tibs.2016.11.002. Epub 2017 Jan 12. Review.

PMID:
28089412
20.

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.

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