ArticleNucleic acids research2013
MetalPDB: a database of metal sites in biological macromolecular structures.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 74 papers.
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Who cites it
74 citing papers in PubMed.
- Geometric deep learning-enabled metal-binding site identification and grafting.Fundamental research · 2026Article
- Computational Analysis of Iron-binding Proteins in the Mutational Landscape of Cancer.Biological trace element research · 2026Article
- Master of Metals2: a graph neural network based architecture for the prediction of zinc binding sites in protein structures.Briefings in bioinformatics · 2026Article
- Random heteropolymers as enzyme mimics.Nature · 2026Article
- MetAP DB and Metal-FP: a database and fingerprint framework for advancing metal-based drug discovery.Journal of computer-aided molecular design · 2025Article
- A bioinformatics approach to design minimal biomimetic metal-binding peptides.Communications chemistry · 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
- Benchmarking Zinc-Binding Site Predictors: A Comparative Analysis of Structure-Based Approaches.Journal of chemical information and modeling · 2025Article
- Recent advances and future challenges in predictive modeling of metalloproteins by artificial intelligence.Molecules and cells · 2025Review
- PinMyMetal: a hybrid learning system to accurately model transition metal binding sites in macromolecules.Nature communications · 2025Article
- Amino Acid Complexation Fractionates Nickel Isotopes: Implications for Tracing Nickel Cycling in the Environment.Environmental science & technology letters · 2025Article
- Computational and experimental mapping of the allosteric network of two manganese ABC transporters.Protein science : a publication of the Protein Society · 2025Article
- Predicting the location of coordinated metal ion-ligand binding sites using geometry-aware graph neural networks.Computational and structural biotechnology journal · 2025Article
- Bacterial Metallostasis: Metal Sensing, Metalloproteome Remodeling, and Metal Trafficking.Chemical reviews · 2024Review
- Putative retina metal/metalloid-binding proteins: molecular functions, biological processes and retina disease associations.Metallomics : integrated biometal science · 2024Article
- A database overview of metal-coordination distances in metalloproteins.Acta crystallographica. Section D, Structural biology · 2024Article
- MetalHawk: Enhanced Classification of Metal Coordination Geometries by Artificial Neural Networks.Journal of chemical information and modeling · 2024Article
- Characterization of the Zinc Uptake Repressor (Zur) fromBiochemistry · 2024Article
- Thermodynamics of Metal-Acetate Interactions.The journal of physical chemistry. B · 2024Article
- Fe(II), Mn(II), and Zn(II) Binding to the C-Terminal Region of FeoB Protein: An Insight into the Coordination Chemistry and Specificity of theInorganic chemistry · 2023Article
14 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present here MetalPDB (freely accessible at http://metalweb.cerm.unifi.it), a novel resource aimed at conveying the information available on the three-dimensional (3D) structures of metal-binding biological macromolecules in a consistent and effective manner. This is achieved through the systematic and automated representation of metal-binding sites in proteins and nucleic acids by way of Minimal Functional Sites (MFSs). MFSs are 3D templates that describe the local environment around the metal(s) independently of the larger context of the macromolecular structure embedding the site(s), and are the central objects of MetalPDB design. MFSs are grouped into equistructural (broadly defined as sites found in corresponding positions in similar structures) and equivalent sites (equistructural sites that contain the same metals), allowing users to easily analyse similarities and variations in metal-macromolecule interactions, and to link them to functional information. The web interface of MetalPDB allows access to a comprehensive overview of metal-containing biological structures, providing a basis to investigate the basic principles governing the properties of these systems. MetalPDB is updated monthly in an automated manner.
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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.