ArticleACS omega2020
Upgraded AMBER Force Field for Zinc-Binding Residues and Ligands for Predicting Structural Properties and Binding Affinities in Zinc-Proteins.
Article in ACS omega, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Restoring Meropenem Activity Against VIM-1-Producing Klebsiella pneumoniae Through Zinc-Binding Ligands.Chembiochem : a European journal of chemical biology · 2026Article
- The Last Mile Problem: A Critical Assessment of Physics-Based and AI Tools for Small Molecule Binding Prediction in Virtual Screening.Journal of chemical information and modeling · 2026Article
- Poly(ADP-ribose)polymerase 2 is zinc-dependent enzyme and nucleosome reorganizer.Cellular and molecular life sciences : CMLS · 2025Article
- Development of a New AMBER Force Field for Cysteine and Histidine Cadmium-Binding Proteins and Its Validation Through QM/MM MD Simulations.Journal of computational chemistry · 2025Article
- Protocols for Metallo- and Serine-β-Lactamase Free Energy Predictions: Insights from Cross-Class Inhibitors.The journal of physical chemistry. B · 2024Article
- A database overview of metal-coordination distances in metalloproteins.Acta crystallographica. Section D, Structural biology · 2024Article
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- New Insights into the LANCL2-Pharmaceutics · 2023Article
- Carbonic Anhydrase Robustness for Use in Nanoscale COACS omega · 2023Article
- Repurposing of World-Approved Drugs for Potential Inhibition against Human Carbonic Anhydrase I: A Computational Study.International journal of molecular sciences · 2023Article
- Molecular Mechanism of Zinc-Dependent Oligomerization of Alzheimer's Amyloid-β with Taiwan (D7H) Mutation.International journal of molecular sciences · 2023Article
- Zn-dependent β-amyloid Aggregation and its Reversal by the Tetrapeptide HAEE.Aging and disease · 2023Article
- A Comparison of Bonded and Nonbonded Zinc(II) Force Fields with NMR Data.International journal of molecular sciences · 2023Article
- A Zn-dependent structural transition of SOD1 modulates its ability to undergo phase separation.The EMBO journal · 2023Article
- Development of Hydroxamic Acid Compounds for Inhibition of Metallo-β-Lactamase fromInternational journal of molecular sciences · 2022Article
- Probing the competitive inhibitor efficacy of frog-skin alpha helical AMPs identified against ACE2 binding to SARS-CoV-2 S1 spike protein as therapeutic scaffold to prevent COVID-19.Journal of molecular modeling · 2022Article
- Zinc Induced AβInternational journal of molecular sciences · 2021Article
- Insights into the Dynamics of the Human Zinc Transporter ZnT8 by MD Simulations.Journal of chemical information and modeling · 2021Article
- Recent Developments in Free Energy Calculations for Drug Discovery.Frontiers in molecular biosciences · 2021Review
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We developed a novel force field in the context of AMBER parameterization for glutamate and aspartate zinc(II)-binding residues. The interaction between the zinc ion and the coordinating atoms is represented by a spherical nonbonded parameterization. The polarization effect due to the zinc ion has been taken into account by redefining the atomic charges on the residues through accurate quantum mechanical calculations. The new zinc-binding ASP and GLU residues, along with the CYS and HIS zinc-binding residues, parameterized in a recent work [Macchiagodena M.;J. Chem. Inf. Model.2019, 59, 3803-3816], allow users to reliably simulate 96% of the Zn-proteins available in the Protein Data Bank. The upgraded force field for zinc(II)-bound residues has been tested performing molecular dynamics simulations with an explicit solvent and comparing the structural information with experimental data for five different proteins binding zinc(II) with GLU, ASP, HIS, and CYS. We further validated our approach by evaluating the binding free energy of (
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