Validation of Structures in the Protein Data Bank.
Validation of Structures in the Protein Data Bank.
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DOI：
10.1016/j.str.2017.10.009
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发表时间：
2017-12-05
期刊：
影响因子：
--
通讯作者：
Kleywegt GJ
中科院分区：
文献类型：
--
作者：
Gore S;Sanz García E;Hendrickx PMS;Gutmanas A;Westbrook JD;Yang H;Feng Z;Baskaran K;Berrisford JM;Hudson BP;Ikegawa Y;Kobayashi N;Lawson CL;Mading S;Mak L;Mukhopadhyay A;Oldfield TJ;Patwardhan A;Peisach E;Sahni G;Sekharan MR;Sen S;Shao C;Smart OS;Ulrich EL;Yamashita R;Quesada M;Young JY;Nakamura H;Markley JL;Berman HM;Burley SK;Velankar S;Kleywegt GJ
Worldwide PDB最近推出了一个沉积、生物固化和验证工具：OneDep。在OneDep数据处理的各个阶段，生成生物大分子三维结构的验证报告。这些报告是基于代表晶体学、核磁共振和冷冻电子显微镜社区的专家工作组的建议。这些报告提供了有用的指标，存款人可以评估实验数据的质量，结构模型，以及它们之间的配合。验证模块也可以作为独立的Web服务器和可编程访问的Web服务。越来越多的期刊要求官方的wwPDB验证报告（在biocuration制作）伴随着描述大分子结构的手稿。在结构公开发布后，验证报告成为公共PDB存档的一部分。PDB档案中蛋白质的几何质量分数在过去十年中有所改善。验证报告可在PDB中获得X射线，NMR和EM结构初步报告，在沉积，独立服务器和编程时获得生物定位的官方报告应与手稿一起提交蛋白质结构的质量指标在过去十年中有所改善戈尔et al.描述社区推荐的验证报告，由wwPDB在PDB提交的沉积和生物固化时生成，并集成到公开发布的PDB条目的档案中。作者还表明，蛋白质结构的质量在过去十年中有所改善。
The Worldwide PDB recently launched a deposition, biocuration, and validation tool: OneDep. At various stages of OneDep data processing, validation reports for three-dimensional structures of biological macromolecules are produced. These reports are based on recommendations of expert task forces representing crystallography, nuclear magnetic resonance, and cryoelectron microscopy communities. The reports provide useful metrics with which depositors can evaluate the quality of the experimental data, the structural model, and the fit between them. The validation module is also available as a stand-alone web server and as a programmatically accessible web service. A growing number of journals require the official wwPDB validation reports (produced at biocuration) to accompany manuscripts describing macromolecular structures. Upon public release of the structure, the validation report becomes part of the public PDB archive. Geometric quality scores for proteins in the PDB archive have improved over the past decade. Validation reports are available for X-ray, NMR, and EM structures in the PDB Preliminary reports obtained at deposition, stand-alone servers, and programmatically Official reports from biocuration should be submitted with manuscripts Quality metrics for protein structures have improved over the past decade Gore et al. describe the community-recommended validation reports, produced by wwPDB at deposition and biocuration of PDB submissions, and integrated into the archive of publicly released PDB entries. The authors also show that the quality of protein structures has improved over the last decade.
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影响因子：
3
作者：
Kirchner DK;Güntert P
通讯作者：
Güntert P
影响因子：
5.7
作者：
Adams, Paul D.;Aertgeerts, Kathleen;Bauer, Cary;Bell, Jeffrey A.;Berman, Helen M.;Bhat, Talapady N.;Blaney, Jeff M.;Bolton, Evan;Bricogne, Gerard;Brown, David;Burley, Stephen K.;Case, David A.;Clark, Kirk L.;Darden, Tom;Emsley, Paul;Feher, Victoria A.;Feng, Zukang;Groom, Colin R.;Harris, Seth F.;Hendle, Jorg;Holder, Thomas;Joachimiak, Andrzej;Kleywegt, Gerard J.;Krojer, Tobias;Marcotrigiano, Joseph;Mark, Alan E.;Markley, John L.;Miller, Matthew;Minor, Wladek;Montelione, Gaetano T.;Murshudov, Garib;Nakagawa, Atsushi;Nakamura, Haruki;Nicholls, Anthony;Nicklaus, Marc;Nolte, Robert T.;Padyana, Anil K.;Peishoff, Catherine E.;Pieniazek, Susan;Read, Randy J.;Shao, Chenghua;Sheriff, Steven;Smart, Oliver;Soisson, Stephen;Spurlino, John;Stouch, Terry;Svobodova, Radka;Tempel, Wolfram;Terwilliger, Thomas C.;Tronrud, Dale;Velankar, Sameer;Ward, Suzanna C.;Warren, Gregory L.;Westbrook, John D.;Williams, Pamela;Yang, Huanwang;Young, Jasmine
通讯作者：
Young, Jasmine
DOI：
10.1107/s0907444909052925
发表时间：
2010-02
期刊：
Acta crystallographica. Section D, Biological crystallography
影响因子：
--
作者：
Adams PD;Afonine PV;Bunkóczi G;Chen VB;Davis IW;Echols N;Headd JJ;Hung LW;Kapral GJ;Grosse-Kunstleve RW;McCoy AJ;Moriarty NW;Oeffner R;Read RJ;Richardson DC;Richardson JS;Terwilliger TC;Zwart PH
通讯作者：
Zwart PH
DOI：
10.1107/s0907444909042073
发表时间：
2010-01
期刊：
Acta crystallographica. Section D, Biological crystallography
影响因子：
--
作者：
Chen VB;Arendall WB 3rd;Headd JJ;Keedy DA;Immormino RM;Kapral GJ;Murray LW;Richardson JS;Richardson DC
通讯作者：
Richardson DC
DOI：
10.1107/s0907444911050359
发表时间：
2012-04
期刊：
Acta crystallographica. Section D, Biological crystallography
影响因子：
--
作者：
Gore S;Velankar S;Kleywegt GJ
通讯作者：
Kleywegt GJ