Outcome of the first wwPDB/CCDC/D3R ligand validation workshop

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 and Young, Jasmine (2016) Outcome of the first wwPDB/CCDC/D3R ligand validation workshop. Structure, 24 4: 502-508. doi:10.1016/j.str.2016.02.017


Author 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
Title Outcome of the first wwPDB/CCDC/D3R ligand validation workshop
Journal name Structure   Check publisher's open access policy
ISSN 0969-2126
1878-4186
Publication date 2016-04-05
Sub-type Critical review of research, literature review, critical commentary
DOI 10.1016/j.str.2016.02.017
Open Access Status Not yet assessed
Volume 24
Issue 4
Start page 502
End page 508
Total pages 7
Place of publication Cambridge, MA, United States
Publisher Cell Press
Collection year 2017
Language eng
Abstract 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 (PDB) archive, ∼75% include at least one non-polymeric ligand. Ligand geometrical and stereochemical quality, the suitability of ligand models for in silico drug discovery and 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 PDB/Cambridge Crystallographic Data Center/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 PDB? 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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Institutional Status UQ

Document type: Journal Article
Sub-type: Critical review of research, literature review, critical commentary
Collections: HERDC Pre-Audit
School of Chemistry and Molecular Biosciences
 
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