ArticleActa crystallographica. Section D, Structural biology2016
Improved ligand geometries in crystallographic refinement using AFITT in PHENIX.
Article in Acta crystallographica. Section D, Structural biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- KNexPHENIX: A PHENIX-Based Workflow for Improving Cryo-EM and Crystallographic Structural Models.Journal of chemical information and modeling · 2026Article
- The Untangle Challenge for accurate ensemble models.bioRxiv : the preprint server for biology · 2026Article
- High-Risk Neuroblastoma Stage 4 (NBS4): Developing a Medicinal Chemistry Multi-Target Drug Approach.Molecules (Basel, Switzerland) · 2025Article
- A Distributional Model of Bound Ligand Conformational Strain: From Small Molecules up to Large Peptidic Macrocycles.Journal of medicinal chemistry · 2023Article
- In situ ligand restraints from quantum-mechanical methods.Acta crystallographica. Section D, Structural biology · 2023Article
- Protein Frameworks with Thiacalixarene and Zinc.Crystal growth & design · 2022Article
- 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
- Modelling covalent linkages in CCP4.Acta crystallographica. Section D, Structural biology · 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
- Fragment Pose Prediction Using Non-equilibrium Candidate Monte Carlo and Molecular Dynamics Simulations.Journal of chemical theory and computation · 2020Article
- The role of the light chain in the structure and binding activity of two cattle antibodies that neutralize bovine respiratory syncytial virus.Molecular immunology · 2019Article
- Structure-Based in Silico Screening Identifies a Potent Ebolavirus Inhibitor from a Traditional Chinese Medicine Library.Journal of medicinal chemistry · 2019Article
- qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps.Journal of medicinal chemistry · 2018Article
- 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
- Validation of ligands in macromolecular structures determined by X-ray crystallography.Acta crystallographica. Section D, Structural biology · 2018Article
- Target Identification and Mode of Action of Four Chemically Divergent Drugs against Ebolavirus Infection.Journal of medicinal chemistry · 2018Article
- Conformational energy range of ligands in protein crystal structures: The difficult quest for accurate understanding.Journal of molecular recognition : JMR · 2017Review
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7 authors.
Funding
Abstract
Modern crystal structure refinement programs rely on geometry restraints to overcome the challenge of a low data-to-parameter ratio. While the classical Engh and Huber restraints work well for standard amino-acid residues, the chemical complexity of small-molecule ligands presents a particular challenge. Most current approaches either limit ligand restraints to those that can be readily described in the Crystallographic Information File (CIF) format, thus sacrificing chemical flexibility and energetic accuracy, or they employ protocols that substantially lengthen the refinement time, potentially hindering rapid automated refinement workflows. PHENIX-AFITT refinement uses a full molecular-mechanics force field for user-selected small-molecule ligands during refinement, eliminating the potentially difficult problem of finding or generating high-quality geometry restraints. It is fully integrated with a standard refinement protocol and requires practically no additional steps from the user, making it ideal for high-throughput workflows. PHENIX-AFITT refinements also handle multiple ligands in a single model, alternate conformations and covalently bound ligands. Here, the results of combining AFITT and the PHENIX software suite on a data set of 189 protein-ligand PDB structures are presented. Refinements using PHENIX-AFITT significantly reduce ligand conformational energy and lead to improved geometries without detriment to the fit to the experimental data. For the data presented, PHENIX-AFITT refinements result in more chemically accurate models for small-molecule ligands.
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