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 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
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:	05 Nov 2024 10:52 UTC
Resource URI:	https://kar.kent.ac.uk/id/eprint/60030 (The current URI for this page, for reference purposes)

University of Kent Author Information

Brown, David G..

Creator's ORCID:	https://orcid.org/0000-0003-4605-4779
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