ArticleStructure (London, England : 1993)2011
Reintroducing electrostatics into macromolecular crystallographic refinement: application to neutron crystallography and DNA hydration.
Article in Structure (London, England : 1993), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 35 citations in OpenAlex.
- Crystal Polymorph Search in theCrystal growth & design · 2024Article
- A generalized Kirkwood implicit solvent for the polarizable AMOEBA protein model.The Journal of chemical physics · 2023Article
- Structural studies of protein-nucleic acid complexes: A brief overview of the selected techniques.Computational and structural biotechnology journal · 2023Review
- Macromolecular refinement of X-ray and cryoelectron microscopy structures with Phenix/OPLS3e for improved structure and ligand quality.Structure (London, England : 1993) · 2021Article
- Refinement of RNA Structures Using Amber Force Fields.Crystals · 2021Article
- Water structure around a left-handed Z-DNA fragment analyzed by cryo neutron crystallography.Nucleic acids research · 2021Article
- Structural Insights into Hearing Loss Genetics from Polarizable Protein Repacking.Biophysical journal · 2019Article
- Article
- Temperature-Induced Replacement of Phosphate Proton with Metal Ion Captured in Neutron Structures of A-DNA.Structure (London, England : 1993) · 2018Article
- Cryo-neutron crystallographic data collection and preliminary refinement of left-handed Z-DNA d(CGCGCG).Acta crystallographica. Section F, Structural biology communications · 2018Article
- Review
- Computational Methodologies for Real-Space Structural Refinement of Large Macromolecular Complexes.Annual review of biophysics · 2016Review
- Diffraction Techniques in Structural Biology.Current protocols in nucleic acid chemistry · 2016Review
- High-resolution crystal structures of protein helices reconciled with three-centered hydrogen bonds and multipole electrostatics.PloS one · 2015Article
- Deformable elastic network refinement for low-resolution macromolecular crystallography.Acta crystallographica. Section D, Biological crystallography · 2014Article
- Protein-ligand cocrystal structures: we can do better.ACS medicinal chemistry letters · 2014Article
- Phosphates in the Z-DNA dodecamer are flexible, but their P-SAD signal is sufficient for structure solution.Acta crystallographica. Section D, Biological crystallography · 2014Article
- Seeing the chemistry in biology with neutron crystallography.Physical chemistry chemical physics : PCCP · 2013Article
- Limiting assumptions in molecular modeling: electrostatics.Journal of computer-aided molecular design · 2013Article
- Advances, interactions, and future developments in the CNS, Phenix, and Rosetta structural biology software systems.Annual review of biophysics · 2013Review
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7 authors at 4 institutions in 1 country.
Funding
Abstract
Most current crystallographic structure refinements augment the diffraction data with a priori information consisting of bond, angle, dihedral, planarity restraints, and atomic repulsion based on the Pauli exclusion principle. Yet, electrostatics and van der Waals attraction are physical forces that provide additional a priori information. Here, we assess the inclusion of electrostatics for the force field used for all-atom (including hydrogen) joint neutron/X-ray refinement. Two DNA and a protein crystal structure were refined against joint neutron/X-ray diffraction data sets using force fields without electrostatics or with electrostatics. Hydrogen-bond orientation/geometry favors the inclusion of electrostatics. Refinement of Z-DNA with electrostatics leads to a hypothesis for the entropic stabilization of Z-DNA that may partly explain the thermodynamics of converting the B form of DNA to its Z form. Thus, inclusion of electrostatics assists joint neutron/X-ray refinements, especially for placing and orienting hydrogen atoms.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.