Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop.
Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop.
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DOI：
10.1016/j.str.2016.02.017
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发表时间：
2016-04-05
期刊：
影响因子：
5.7
通讯作者：
Young, Jasmine
中科院分区：
文献类型：
--
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
与生物大分子（蛋白质和核酸）结合的配体的晶体学研究代表了有关药物-靶标相互作用的重要信息来源，为大分子和配体之间形成复合物的物理化学提供了原子水平的见解。在蛋白质数据库档案中现存的超过115，000个条目中，约75%包括至少一个非聚合配体。配体的几何和立体化学质量，在计算机药物发现/设计的配体模型的适用性，以及配体模型的电子密度图的拟合优度在整个档案中变化很大。我们描述了2015年7月30日至31日在罗格斯大学结构生物信息学研究合作实验室举行的第一届全球蛋白质数据库/剑桥晶体学数据中心/药物设计数据资源（wwPDB/CCDC/D3 R）配体验证研讨会的程序和结论。来自工业界的蛋白质晶体学专家与非营利和营利的晶体学软件提供商以及计算化学和数据存档专家一起讨论并提出最佳实践建议，这些建议由一系列对大分子-配体复合物结构研究至关重要的问题构成。关于结合配体的哪些数据应该在蛋白质数据库中存档？如何最好地代表配体？应如何验证大分子-配体复合物的结构模型？生物大分子结构研究的出版物应附带哪些补充信息？提供了针对每个问题制定的最佳实践的共识建议，以及有关实施的一些详细信息。还列举了研讨会上讨论但尚未解决的重要问题。
Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) represent an important source of information concerning drug-target interactions, providing atomic level insights into the physical chemistry of complex formation between macromolecules and ligands. Of the more than 115,000 entries extant in the Protein Data Bank archive, ~75% include at least one non-polymeric ligand. Ligand geometrical and stereochemical quality, the suitability of ligand models for in silico drug discovery/design, and the goodness-of-fit of ligand models to electron density maps vary widely across the archive. We describe the proceedings and conclusions from the first Worldwide Protein Data Bank/Cambridge Crystallographic Data Centre/Drug Design Data Resource (wwPDB/CCDC/D3R) Ligand Validation Workshop held at the Research Collaboratory for Structural Bioinformatics at Rutgers University on July 30–31, 2015. Experts in protein crystallography from academe and industry came together with non-profit and for-profit software providers for crystallography and with experts in computational chemistry and data archiving to discuss and make recommendations on best practices, as framed by a series of questions central to structural studies of macromolecule-ligand complexes. What data concerning bound ligands should be archived in the Protein Data Bank? How should the ligands be best represented? How should structural models of macromolecule-ligand complexes be validated? What supplementary information should accompany publications of structural studies of biological macromolecules? Consensus recommendations on best practices developed in response to each of these questions are provided, together with some details regarding implementation. Important issues addressed but not resolved at the workshop are also enumerated.
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DOI：
10.1107/s0907444912044423
发表时间：
2013-02-01
影响因子：
2.2
作者：
Pozharski, Edwin;Weichenberger, Christian X.;Rupp, Bernhard
通讯作者：
Rupp, Bernhard
影响因子：
14.9
作者：
Sehnal, David;Varekova, Radka Svobodova;Koca, Jaroslav
通讯作者：
Koca, Jaroslav
影响因子：
14.9
作者：
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
通讯作者：
Berman HM
影响因子：
5.6
作者：
Sitzmann M;Weidlich IE;Filippov IV;Liao C;Peach ML;Ihlenfeldt WD;Karki RG;Borodina YV;Cachau RE;Nicklaus MC
通讯作者：
Nicklaus MC
影响因子：
3.5
作者：
Liebeschuetz, John;Hennemann, Jana;Olsson, Tjelvar;Groom, Colin R.
通讯作者：
Groom, Colin R.