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 G., and others. (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: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) (KAR id:60030)
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Official URL: http://dx.doi.org/10.1016/j.str.2016.02.017 |
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 |
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DOI/Identification number: | 10.1016/j.str.2016.02.017 |
Subjects: | Q Science > QD Chemistry > QD431 Organic Chemistry- Biochemistry- Proteins, peptides, amino acids |
Divisions: | Divisions > Division of Natural Sciences > Biosciences |
Depositing User: | David Brown |
Date Deposited: | 23 Jan 2017 13:58 UTC |
Last Modified: | 17 Aug 2022 12:21 UTC |
Resource URI: | https://kar.kent.ac.uk/id/eprint/60030 (The current URI for this page, for reference purposes) |
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