ArticleActa crystallographica. Section D, Structural biology2017
Ligand fitting with CCP4.
Article in Acta crystallographica. Section D, Structural biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed.
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- Expanding Automated Multiconformer Ligand Modeling to Macrocycles and Fragments.bioRxiv : the preprint server for biology · 2025Article
- Reanalysis of a μ opioid receptor crystal structure reveals a covalent adduct with BU72.BMC biology · 2023Article
- The CCP4 suite: integrative software for macromolecular crystallography.Acta crystallographica. Section D, Structural biology · 2023Article
- CMM-An enhanced platform for interactive validation of metal binding sites.Protein science : a publication of the Protein Society · 2023Article
- Determination of oligosaccharide product distributions of PL7 alginate lyases by their structural elements.Communications biology · 2022Article
- Raw diffraction data are our ground truth from which all subsequent workflows develop.Acta crystallographica. Section D, Structural biology · 2022Article
- Updated restraint dictionaries for carbohydrates in the pyranose form.Acta crystallographica. Section D, Structural biology · 2022Article
- Optimisation of Neuraminidase Expression for Use in Drug Discovery by Using HEK293-6E Cells.Viruses · 2021Article
- The missing link: covalent linkages in structural models.Acta crystallographica. Section D, Structural biology · 2021Article
- Structural adaptation of vertebrate endonuclease G for 5-hydroxymethylcytosine recognition and function.Nucleic acids research · 2020Article
- Computation-guided analysis of paroxetine binding to hSERT reveals functionally important structural elements and dynamics.Neuropharmacology · 2019Article
- Review
- High-throughput quantum-mechanics/molecular-mechanics (ONIOM) macromolecular crystallographic refinement with PHENIX/DivCon: the impact of mixed Hamiltonian methods on ligand and protein structure.Acta crystallographica. Section D, Structural biology · 2018Article
- Discovery of a Short-Chain Dehydrogenase from Catharanthus roseus that Produces a New Monoterpene Indole Alkaloid.Chembiochem : a European journal of chemical biology · 2018Article
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Abstract
Crystal structures of protein-ligand complexes are often used to infer biology and inform structure-based drug discovery. Hence, it is important to build accurate, reliable models of ligands that give confidence in the interpretation of the respective protein-ligand complex. This paper discusses key stages in the ligand-fitting process, including ligand binding-site identification, ligand description and conformer generation, ligand fitting, refinement and subsequent validation. The CCP4 suite contains a number of software tools that facilitate this task: AceDRG for the creation of ligand descriptions and conformers, Lidia and JLigand for two-dimensional and three-dimensional ligand editing and visual analysis, Coot for density interpretation, ligand fitting, analysis and validation, and REFMAC5 for macromolecular refinement. In addition to recent advancements in automatic carbohydrate building in Coot (LO/Carb) and ligand-validation tools (FLEV), the release of the CCP4i2 GUI provides an integrated solution that streamlines the ligand-fitting workflow, seamlessly passing results from one program to the next. The ligand-fitting process is illustrated using instructive practical examples, including problematic cases such as post-translational modifications, highlighting the need for careful analysis and rigorous validation.
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