Outcome of a workshop on archiving structural models of biological macromolecules.

By Helen M. Berman, Stephen K. Burley, Wah Chiu, Andrej Sali, Alexei Adzhubei, Philip E. Bourne, Stephen H. Bryant, Roland L. Dunbrack, Krzysztof Fidelis, Joachim Frank and 15 more. 2006

64 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology, Structural Biology

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Citations in the corpus

The SWISS-MODEL Repository—new features and functionality (2016, background): “org/) and providing the stable reference code to the model in the manuscript (30,32).”
Outcome of a Workshop on Applications of Protein Models in Biomedical Research (2009, methodology): “Since 2006, only structures that have been determined experimentally are allowed to be deposited in the PDB (Berman et al., 2006).”
The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data (2006, background): “A recent example is the announcement of the policy for the archiving of in silico models ( 19 ).”
Structural genomics is the largest contributor of novel structural leverage (2009, background): “Our restriction to E-values B 10 implies that the inferred structural models are of relatively high reliability and cover most of the aligned regions [16, 25]; higher leverage and coverage can be achieved at the expense of accuracy [3, 17, 27, 33].”
A public database of macromolecular diffraction experiments. (2016, background): “In the 1990s, the PDB began requesting the submission of additional metadata, which were included in each PDB entry header, and since 2006 the deposition of structure-factor files for X-ray diffraction models has been mandatory (Berman et al., 2006).”
Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive (2017, background): “A workshop held in 2005 led to adoption of the policy that purely in silico structural models do not belong in the PDB [25], and, instead, an independent repository should be created to archive computed models elsewhere.”
Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop (2015, unknown): “In addition, the wwPDB and, in later years, the Structural Biology Knowledgebase (SBKB), spearheaded three workshops focused on validation, archiving, and dissemination of comparative protein structure models (Berman et al., 2006; Schwede et al., 2009).”
Thirty years of environmental health research--and growing. (1996, methodology): “The assessment of the accuracy and reliability of experimental and theoretical models of protein structures is a necessary task that needs to be addressed regularly and in particular, it is essential for maintaining integrity, consistency and reliability of public structure repositories (2).”
The Protein Model Portal (2008, background): “Consequently, a community workshop held at Rutgers on archiving structural models of biological macromolecules has recommended no longer accepting models as part of the PDB archive, and to establish a portal for protein model information [21].”
Protein Modelling: What Happened to the “Protein Structure Gap”? (2013, unknown): “However, since coordinates derived by theoretical modeling cannot be deposited in the PDB (Berman et al., 2006), many manuscripts reporting results of theoretical modeling or simulations are published without making the models available.”