ArticleActa crystallographica. Section D, Biological crystallography2014
Accurate macromolecular crystallographic refinement: incorporation of the linear scaling, semiempirical quantum-mechanics program DivCon into the PHENIX refinement package.
Article in Acta crystallographica. Section D, Biological crystallography, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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29 citing papers in PubMed.
- AQuaRef: machine learning accelerated quantum refinement of protein structures.Nature communications · 2025Article
- Article
- Accelerating reliable multiscale quantum refinement of protein-drug systems enabled by machine learning.Nature communications · 2024Article
- Continuous Validation Across Macromolecular Structure Determination Process.Nihon Kessho Gakkai shi · 2023Article
- A Distributional Model of Bound Ligand Conformational Strain: From Small Molecules up to Large Peptidic Macrocycles.Journal of medicinal chemistry · 2023Article
- Towards Consistency in Geometry Restraints for Carbohydrates in the Pyranose form: Modern Dictionary Generators Reviewed.Current medicinal chemistry · 2022Article
- Macromolecular refinement of X-ray and cryoelectron microscopy structures with Phenix/OPLS3e for improved structure and ligand quality.Structure (London, England : 1993) · 2021Article
- The critical role of QM/MM X-ray refinement and accurate tautomer/protomer determination in structure-based drug design.Journal of computer-aided molecular design · 2021Article
- MovableType Software for Fast Free Energy-Based Virtual Screening: Protocol Development, Deployment, Validation, and Assessment.Journal of chemical information and modeling · 2020Article
- Quantum refinement with multiple conformations: application to the P-cluster in nitrogenase.Acta crystallographica. Section D, Structural biology · 2020Article
- fragHAR: towardsIUCrJ · 2020Article
- Refinement of protein structures using a combination of quantum-mechanical calculations with neutron and X-ray crystallographic data.Acta crystallographica. Section D, Structural biology · 2019Article
- Predicting protein-ligand binding affinity and correcting crystal structures with quantum mechanical calculations: lactate dehydrogenase A.Chemical science · 2019Article
- 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
- Noncovalent interactions dominate dynamic heme distortion in cytochrome P450 4B1.The Journal of biological chemistry · 2018Article
- Validation of ligands in macromolecular structures determined by X-ray crystallography.Acta crystallographica. Section D, Structural biology · 2018Article
- Solving the scalability issue in quantum-based refinement: Q|R#1.Acta crystallographica. Section D, Structural biology · 2017Article
- Conformational energy range of ligands in protein crystal structures: The difficult quest for accurate understanding.Journal of molecular recognition : JMR · 2017Review
- Quantum crystallography.Chemical science · 2017Review
- The Crystal Structure of Cytochrome P450 4B1 (CYP4B1) Monooxygenase Complexed with Octane Discloses Several Structural Adaptations for ω-Hydroxylation.The Journal of biological chemistry · 2017Article
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5 authors.
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Abstract
Macromolecular crystallographic refinement relies on sometimes dubious stereochemical restraints and rudimentary energy functionals to ensure the correct geometry of the model of the macromolecule and any covalently bound ligand(s). The ligand stereochemical restraint file (CIF) requires a priori understanding of the ligand geometry within the active site, and creation of the CIF is often an error-prone process owing to the great variety of potential ligand chemistry and structure. Stereochemical restraints have been replaced with more robust functionals through the integration of the linear-scaling, semiempirical quantum-mechanics (SE-QM) program DivCon with the PHENIX X-ray refinement engine. The PHENIX/DivCon package has been thoroughly validated on a population of 50 protein-ligand Protein Data Bank (PDB) structures with a range of resolutions and chemistry. The PDB structures used for the validation were originally refined utilizing various refinement packages and were published within the past five years. PHENIX/DivCon does not utilize CIF(s), link restraints and other parameters for refinement and hence it does not make as many a priori assumptions about the model. Across the entire population, the method results in reasonable ligand geometries and low ligand strains, even when the original refinement exhibited difficulties, indicating that PHENIX/DivCon is applicable to both single-structure and high-throughput crystallography.
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