ArticleStructure (London, England : 1993)2016
Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop.
Article in Structure (London, England : 1993), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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43 citing papers in PubMed.
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- Validated ligand geometries for macromolecular refinement restraints and molecular mechanics force fields.bioRxiv : the preprint server for biology · 2025Article
- Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge.Nature methods · 2024Article
- Continuous Validation Across Macromolecular Structure Determination Process.Nihon Kessho Gakkai shi · 2023Article
- Protein Data Bank: A Comprehensive Review of 3D Structure Holdings and Worldwide Utilization by Researchers, Educators, and Students.Biomolecules · 2022Review
- Group depositions to the Protein Data Bank need adequate presentation and different archiving protocol.Protein science : a publication of the Protein Society · 2022Article
- Simplified quality assessment for small-molecule ligands in the Protein Data Bank.Structure (London, England : 1993) · 2022Article
- Experiences From Developing Software for Large X-Ray Crystallography-Driven Protein-Ligand Studies.Frontiers in molecular biosciences · 2022Article
- Macromolecular refinement of X-ray and cryoelectron microscopy structures with Phenix/OPLS3e for improved structure and ligand quality.Structure (London, England : 1993) · 2021Article
- Recognizing and validating ligands with CheckMyBlob.Nucleic acids research · 2021Article
- 'International journal of molecular sciences · 2021Article
- Open-access data: A cornerstone for artificial intelligence approaches to protein structure prediction.Structure (London, England : 1993) · 2021Review
- Enhanced validation of small-molecule ligands and carbohydrates in the Protein Data Bank.Structure (London, England : 1993) · 2021Article
- The Protein Data Bank Archive.Methods in molecular biology (Clifton, N.J.) · 2021Review
- Structural Analysis of Strigolactone-Related Gene Products.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Automatic recognition of ligands in electron density by machine learning.Bioinformatics (Oxford, England) · 2019Article
- Protein Data Bank: the single global archive for 3D macromolecular structure data.Nucleic acids research · 2019Article
- qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps.Journal of medicinal chemistry · 2018Article
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57 authors.
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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 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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