ReviewBiomolecules2014
QM/MM molecular dynamics studies of metal binding proteins.
Review in Biomolecules, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
What it found
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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.
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Who cites it
22 citing papers in PubMed, 93 citations in OpenAlex.
- Probe-based identification of metal-binding sites using deep learning representations.Nature communications · 2026Article
- Simulation-guided design of peptide-metal coordination interfaces for next-generation metallo-immunotherapy.Nano convergence · 2026Review
- Effects of Nitro-Oxidative Stress on Biomolecules: Part 2-Reactive Molecular Dynamics Simulations.Biomolecules · 2025Review
- The chromatin remodeler SMARCA5 binds to d-block metal supports: Characterization of affinities by IMAC chromatography and QM analysis.PloS one · 2024Article
- Abiraterone Acetate Complexes with Biometals: Synthesis, Characterization in Solid and Solution, and the Nature of Chemical Bonding.Pharmaceutics · 2023Article
- Computational infrared and Raman spectra by hybrid QM/MM techniques: a study on molecular and catalytic material systems.Philosophical transactions. Series A, Mathematical, physical, and engineering sciences · 2023Article
- Structural Characterization ofInternational journal of molecular sciences · 2023Article
- Unravelling the molecular interactions between the SARS-CoV-2 RBD spike protein and various specific monoclonal antibodies.Biochimie · 2022Article
- A multiscale approach to predict the binding mode of metallo beta-lactamase inhibitors.Proteins · 2022Article
- Transcriptomic and Drug Discovery Analyses Reveal Natural Compounds Targeting the KDM4 Subfamily as Promising Adjuvant Treatments in Cancer.Frontiers in genetics · 2022Article
- Frontiers of metal-coordinating drug design.Expert opinion on drug discovery · 2021Review
- Targeting Orthosteric and Allosteric Pockets of Aromatase via Dual-Mode Novel Azole Inhibitors.ACS medicinal chemistry letters · 2020Article
- Copper trafficking in eukaryotic systems: current knowledge from experimental and computational efforts.Current opinion in structural biology · 2019Review
- A Fragmenting Protocol with Explicit Hydration for Calculation of Binding Enthalpies of Target-Ligand Complexes at a Quantum Mechanical Level.International journal of molecular sciences · 2019Article
- Unraveling the Impact of Cysteine-to-Serine Mutations on the Structural and Functional Properties of Cu(I)-Binding Proteins.International journal of molecular sciences · 2019Article
- Computational Approach to Molecular Catalysis by 3d Transition Metals: Challenges and Opportunities.Chemical reviews · 2019Article
- Unraveling the Molecular Mechanism of Pre-mRNA Splicing From Multi-Scale Simulations.Frontiers in molecular biosciences · 2019Article
- Quantum mechanics implementation in drug-design workflows: does it really help?Drug design, development and therapy · 2017Review
- Hydrogenase Enzymes and Their Synthetic Models: The Role of Metal Hydrides.Chemical reviews · 2016Review
- Cooperative motion of a key positively charged residue and metal ions for DNA replication catalyzed by human DNA Polymerase-η.Nucleic acids research · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 2 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Mixed quantum-classical (quantum mechanical/molecular mechanical (QM/MM)) simulations have strongly contributed to providing insights into the understanding of several structural and mechanistic aspects of biological molecules. They played a particularly important role in metal binding proteins, where the electronic effects of transition metals have to be explicitly taken into account for the correct representation of the underlying biochemical process. In this review, after a brief description of the basic concepts of the QM/MM method, we provide an overview of its capabilities using selected examples taken from our work. Specifically, we will focus on heme peroxidases, metallo-β-lactamases, α-synuclein and ligase ribozymes to show how this approach is capable of describing the catalytic and/or structural role played by transition (Fe, Zn or Cu) and main group (Mg) metals. Applications will reveal how metal ions influence the formation and reduction of high redox intermediates in catalytic cycles and enhance drug metabolism, amyloidogenic aggregate formation and nucleic acid synthesis. In turn, it will become manifest that the protein frame directs and modulates the properties and reactivity of the metal ions.
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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.