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

Adams, Paul D. and Aertgeerts, Kathleen and Bauer, Cary and Bell, Jeffrey A. and Berman, Helen M. and Bhat, Talapady N. and Blaney, Jeff M. and Bolton, Evan and Bricogne, Gerard and Brown, David G. and Burley, Stephen K. and Case, David A. and Clark, Kirk L. and Darden, Tom and Emsley, Paul and Feher, Victoria A. and Feng, Zukang and Groom, Colin R. and Harris, Seth F. and Hendle, Jorg and Holder, Thomas and Joachimiak, Andrzej and Kleywegt, Gerard J. and Krojer, Tobias and Marcotrigiano, Joseph and Mark, Alan E. and Markley, John L. and Miller, Matthew and Minor, Wladek and Montelione, Gaetano T. and Murshudov, Garib and Nakagawa, Atsushi and Nakamura, Haruki and Nicholls, Anthony and Nicklaus, Marc and Nolte, Robert T. and Padyana, Anil K. and Peishoff, Catherine E. and Pieniazek, Susan and Read, Randy J. and Shao, Chenghua and Sheriff, Steven and Smart, Oliver and Soisson, Stephen and Spurlino, John and Stouch, Terry and Svobodova, Radka and Tempel, Wolfram and Terwilliger, Thomas C. and Tronrud, Dale and Velankar, Sameer and Ward, Suzanna C. and Warren, Gregory L. and Westbrook, John D. and Williams, Pamela and Yang, Huanwang and Young, Jasmine (2016) Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop. Structure, 24 (4). pp. 502-508. ISSN 0969-2126. E-ISSN 1878-4186. (doi:https://doi.org/10.1016/j.str.2016.02.017) (Access to this publication is currently restricted. You may be able to access a copy if URLs are provided)

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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 macromoleculeligand 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.

Item Type: Article
Subjects: Q Science > QD Chemistry > QD431 Organic Chemistry- Biochemistry- Proteins, peptides, amino acids
Divisions: Faculties > Sciences > School of Biosciences
Faculties > Sciences > School of Biosciences > Protein Science Group
Depositing User: David Brown
Date Deposited: 23 Jan 2017 13:58 UTC
Last Modified: 24 Jan 2017 11:55 UTC
Resource URI: https://kar.kent.ac.uk/id/eprint/60030 (The current URI for this page, for reference purposes)
Brown, David G.: https://orcid.org/0000-0003-4605-4779
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