ArticleJournal of inorganic biochemistry2010
QM/MM X-ray refinement of zinc metalloenzymes.
Article in Journal of inorganic biochemistry, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
21 citing papers in PubMed.
- A database overview of metal-coordination distances in metalloproteins.Acta crystallographica. Section D, Structural biology · 2024Article
- Tris-(2-pyridyl)-pyrazolyl Borate Zinc(II) Complexes: Synthesis, DNA/Protein Binding and In Vitro Cytotoxicity Studies.Molecules (Basel, Switzerland) · 2021Article
- 'International journal of molecular sciences · 2021Article
- Force Field Parameters for FeMolecules (Basel, Switzerland) · 2021Article
- 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
- Quantum crystallography.Chemical science · 2017Review
- QM/MM investigation of the catalytic mechanism of angiotensin-converting enzyme.Journal of molecular modeling · 2016Article
- Exploration of the zinc finger motif in controlling activity of matrix metalloproteinases.The journal of physical chemistry. B · 2014Article
- Using quantum mechanical approaches to study biological systems.Accounts of chemical research · 2014Article
- Accurate macromolecular crystallographic refinement: incorporation of the linear scaling, semiempirical quantum-mechanics program DivCon into the PHENIX refinement package.Acta crystallographica. Section D, Biological crystallography · 2014Article
- Force field independent metal parameters using a nonbonded dummy model.The journal of physical chemistry. B · 2014Article
- Conformational analysis and parallel QM/MM X-ray refinement of protein bound anti-Alzheimer drug donepezil.Journal of chemical theory and computation · 2013Article
- Solution NMR refinement of a metal ion bound protein using metal ion inclusive restrained molecular dynamics methods.Journal of biomolecular NMR · 2013Article
- Conformational Analysis of Free and Bound Retinoic Acid.Journal of chemical theory and computation · 2012Article
- PDB ligand conformational energies calculated quantum-mechanically.Journal of chemical information and modeling · 2012Article
- QM/MM refinement and analysis of protein bound retinoic acid.Journal of computational chemistry · 2012Article
- Nuclear magnetic resonance signal chemical shifts and molecular simulations: a multidisciplinary approach to modeling copper protein structures.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2012Article
- CSAR benchmark exercise of 2010: combined evaluation across all submitted scoring functions.Journal of chemical information and modeling · 2011Article
- Inhibitor and substrate binding by angiotensin-converting enzyme: quantum mechanical/molecular mechanical molecular dynamics studies.Journal of chemical information and modeling · 2011Article
- A Transferable Non-bonded Pairwise Force Field to Model Zinc Interactions in Metalloproteins.Journal of chemical theory and computation · 2011Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Zinc metalloenzymes play an important role in biology. However, due to the limitation of molecular force field energy restraints used in X-ray refinement at medium or low resolutions, the precise geometry of the zinc coordination environment can be difficult to distinguish from ambiguous electron density maps. Due to the difficulties involved in defining accurate force fields for metal ions, the QM/MM (quantum-mechanical/molecular-mechanical) method provides an attractive and more general alternative for the study and refinement of metalloprotein active sites. Herein we present three examples that indicate that QM/MM based refinement yields a superior description of the crystal structure based on R and R(free) values and on the inspection of the zinc coordination environment. It is concluded that QM/MM refinement is an useful general tool for the improvement of the metal coordination sphere in metalloenzyme active sites.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.