ArticleActa crystallographica. Section D, Structural biology2021
Modelling covalent linkages in CCP4.
Article in Acta crystallographica. Section D, Structural biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- A ubiquitin chain-feeding mechanism for BRCA1-A.Nature communications · 2026Article
- Substrate selectivity of the human RNA mNature · 2026Article
- New targets and procedures for validating the valence geometry of nucleic acid structures.Nucleic acids research · 2026Article
- Template-assisted covalent modification underlies activity of covalent molecular glues.Nature chemical biology · 2024Article
- Specific tRNAs promote mRNA decay by recruiting the CCR4-NOT complex to translating ribosomes.Science (New York, N.Y.) · 2024Article
- Crystallographic fragment-binding studies of the Mycobacterium tuberculosis trifunctional enzyme suggest binding pockets for the tails of the acyl-CoA substrates at its active sites and a potential substrate-channeling path between them.Acta crystallographica. Section D, Structural biology · 2024Article
- Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge.Nature methods · 2024Article
- Neutron crystallographic refinement with REFMAC5 from the CCP4 suite.Acta crystallographica. Section D, Structural biology · 2023Article
- The CCP4 suite: integrative software for macromolecular crystallography.Acta crystallographica. Section D, Structural biology · 2023Article
- Template-assisted covalent modification of DCAF16 underlies activity of BRD4 molecular glue degraders.bioRxiv : the preprint server for biology · 2023Article
- Updated restraint dictionaries for carbohydrates in the pyranose form.Acta crystallographica. Section D, Structural biology · 2022Article
- Towards Consistency in Geometry Restraints for Carbohydrates in the Pyranose form: Modern Dictionary Generators Reviewed.Current medicinal chemistry · 2022Article
- Ten things I `hate' about refinement.Acta crystallographica. Section D, Structural biology · 2021Article
- The missing link: covalent linkages in structural models.Acta crystallographica. Section D, Structural biology · 2021Article
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10 authors.
Funding
Abstract
In this contribution, the current protocols for modelling covalent linkages within the CCP4 suite are considered. The mechanism used for modelling covalent linkages is reviewed: the use of dictionaries for describing changes to stereochemistry as a result of the covalent linkage and the application of link-annotation records to structural models to ensure the correct treatment of individual instances of covalent linkages. Previously, linkage descriptions were lacking in quality compared with those of contemporary component dictionaries. Consequently, AceDRG has been adapted for the generation of link dictionaries of the same quality as for individual components. The approach adopted by AceDRG for the generation of link dictionaries is outlined, which includes associated modifications to the linked components. A number of tools to facilitate the practical modelling of covalent linkages available within the CCP4 suite are described, including a new restraint-dictionary accumulator, the Make Covalent Link tool and AceDRG interface in Coot, the 3D graphical editor JLigand and the mechanisms for dealing with covalent linkages in the CCP4i2 and CCP4 Cloud environments. These integrated solutions streamline and ease the covalent-linkage modelling workflow, seamlessly transferring relevant information between programs. Current recommended practice is elucidated by means of instructive practical examples. By summarizing the different approaches to modelling linkages that are available within the CCP4 suite, limitations and potential pitfalls that may be encountered are highlighted in order to raise awareness, with the intention of improving the quality of future modelled covalent linkages in macromolecular complexes.
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