ArticleJournal of chemical information and modeling2014
AutoDock4(Zn): an improved AutoDock force field for small-molecule docking to zinc metalloproteins.
Article in Journal of chemical information and modeling, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 123 papers.
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Who cites it
123 citing papers in PubMed, 287 citations in OpenAlex.
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- Restoring Meropenem Activity Against VIM-1-Producing Klebsiella pneumoniae Through Zinc-Binding Ligands.Chembiochem : a European journal of chemical biology · 2026Article
- MBind: A Web-Based Platform for Metalloprotein and Nonmetalloprotein Docking with Optional ML Docking Integration.Molecules (Basel, Switzerland) · 2026Article
- Structural and functional characterization of an active site-influencing variant (IMP-1-F218Y) in IMP-1 metallo-β-lactamase.The FEBS journal · 2026Article
- CB-Dock3: an enhanced web server for protein-ligand blind docking.Nucleic acids research · 2026Article
- Design and Synthesis of Phosphonoproline-Proline Bioisosteric Mimetics of Proline Dimers: Pseudopeptide Constructs as Potential Inhibitors of the Zn-Metalloprotease PPEP‑1 Associated withACS medicinal chemistry letters · 2026Article
- Targeting Selectivity: Improving Golgi α-Mannosidase II (GMII) Inhibitors Through In Silico Studies.Biomolecules · 2026Review
- Open-Source Molecular Docking and AI-Augmented Structure-Based Drug Design: Current Workflows, Challenges, and Opportunities.International journal of molecular sciences · 2026Review
- AI-Enhanced Adaptive Virtual Screening Platform Enabling Exploration of 69 Billion Molecules Discovers Structurally Validated FSP1 Inhibitors.bioRxiv : the preprint server for biology · 2026Article
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- Integrative transcriptomics and reverse network pharmacology prioritize DPP4 and Achyranthes bidentata in Barrett's esophagus.PloS one · 2026Article
- Meeko: Molecule Parametrization and Software Interoperability for Docking and Beyond.Journal of chemical information and modeling · 2025Article
- New Dimethylpyridine-3-Carboxamide Derivatives as MMP-13 Inhibitors with Anticancer Activity.Molecules (Basel, Switzerland) · 2025Article
- Structural characterization and inhibition of carbonic anhydrase fromJournal of structural biology: X · 2025Article
- Hybrid quantum/classical docking of covalent and non-covalent ligands with Attracting Cavities.Scientific reports · 2025Article
- Machine learning-based virtual screening and density functional theory characterisation of natural inhibitors targeting mutant PBP2x in Streptococcus pneumoniae.Scientific reports · 2025Article
- Minimalistic Peptide Nanocarriers for Multiple Cancer Drugs.ACS applied bio materials · 2025Article
63 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
Zinc is present in a wide variety of proteins and is important in the metabolism of most organisms. Zinc metalloenzymes are therapeutically relevant targets in diseases such as cancer, heart disease, bacterial infection, and Alzheimer's disease. In most cases a drug molecule targeting such enzymes establishes an interaction that coordinates with the zinc ion. Thus, accurate prediction of the interaction of ligands with zinc is an important aspect of computational docking and virtual screening against zinc containing proteins. We have extended the AutoDock force field to include a specialized potential describing the interactions of zinc-coordinating ligands. This potential describes both the energetic and geometric components of the interaction. The new force field, named AutoDock4Zn, was calibrated on a data set of 292 crystal complexes containing zinc. Redocking experiments show that the force field provides significant improvement in performance in both free energy of binding estimation as well as in root-mean-square deviation from the crystal structure pose. The new force field has been implemented in AutoDock without modification to the source code.
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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.