ArticleMethods in enzymology2020
Implementation of the riding hydrogen model in CCTBX to support the next generation of X-ray and neutron joint refinement in Phenix.
Article in Methods in enzymology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Validated ligand geometries for macromolecular refinement restraints and molecular-mechanics force fields.Acta crystallographica. Section D, Structural biology · 2026Article
- High-resolution X-ray structure of Gln143Asn manganese superoxide dismutase captures multiple hydrogen peroxide-binding sites.Acta crystallographica. Section F, Structural biology communications · 2025Article
- Validated ligand geometries for macromolecular refinement restraints and molecular mechanics force fields.bioRxiv : the preprint server for biology · 2025Article
- An ultra-long heavy chain bovine antibody neutralizes SARS-CoV-2 and reacts broadly with sarbecoviruses.bioRxiv : the preprint server for biology · 2025Article
- How Do Gepotidacin and Zoliflodacin Stabilize DNA-Cleavage Complexes with Bacterial Type IIA Topoisomerases? 2. A Single Moving Metal Mechanism.International journal of molecular sciences · 2024Article
- Neutron crystallographic refinement with REFMAC5 from the CCP4 suite.Acta crystallographica. Section D, Structural biology · 2023Article
- Improved joint X-ray and neutron refinement procedure in Phenix.Acta crystallographica. Section D, Structural biology · 2023Article
- Description of peptide bond planarity from high-resolution neutron crystallography.Biophysics and physicobiology · 2023Article
- Re-evaluation of protein neutron crystallography with and without X-ray/neutron joint refinement.IUCrJ · 2022Article
- Discovery of ultrapotent broadly neutralizing antibodies from SARS-CoV-2 elite neutralizers.Cell host & microbe · 2022Article
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Abstract
A fundamental prerequisite for implementing new procedures of atomic model refinement against neutron diffraction data is the efficient handling of hydrogen atoms. The riding hydrogen model, which constrains hydrogen atom parameters to those of the non-hydrogen atoms, is a plausible parameterization for refinements. This work describes the implementation of the riding hydrogen model in the Computational Crystallography Toolbox and in Phenix. Riding hydrogen atoms can be found in several different configurations that are characterized by specific geometries. For each configuration, the hydrogen atom parameterization and the expressions for the gradients of refinement target function with respect to non-hydrogen parameters are described.
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