ArticleNucleic acids research2018
MetalPDB in 2018: a database of metal sites in biological macromolecular structures.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 124 papers.
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Who cites it
124 citing papers in PubMed.
- PrOMet: Accurate and Robust Metal-Binding Site and Type Prediction.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Deep learning based design of buried hydrogen bond networks with HBDesigner.bioRxiv : the preprint server for biology · 2026Article
- Discovery and characterization of a nickel enzyme family that catalyses intermolecular hydride shuttling.Nature chemistry · 2026Article
- The Ascent of Miniproteins.Biochemistry · 2026Review
- Geometric deep learning-enabled metal-binding site identification and grafting.Fundamental research · 2026Article
- Probe-based identification of metal-binding sites using deep learning representations.Nature communications · 2026Article
- Integrated analysis of the redoxome and zinc proteome links ribosomal protein oxidation to zinc homeostasis.Redox biology · 2026Article
- A protein surface-aware multimodal framework for residue-level metal-binding site recognition.Cell reports methods · 2026Article
- Computational Analysis of Iron-binding Proteins in the Mutational Landscape of Cancer.Biological trace element research · 2026Article
- Accurate density functional theory for noncovalent interactions in charged systems.Science advances · 2026Article
- Cytoplasmic localization of pseudouridine synthase 7 facilitates a pseudouridine-dependent enhancement of cellular stress tolerance.Nature communications · 2026Article
- Acclimation of Photosynthesis to the Environment 1 acts as a copper-binding superoxide detoxification enzyme.Nature communications · 2026Article
- Master of Metals2: a graph neural network based architecture for the prediction of zinc binding sites in protein structures.Briefings in bioinformatics · 2026Article
- Structural characterization of metal binding in human tyrosylprotein sulfotransferase 2, TPST2.Scientific reports · 2026Article
- The Human Omnibus of Targetable Pockets.Journal of cheminformatics · 2025Article
- Unlocking Phytoplankton Metallomes with Comparative Analysis of Metal Quotas, Quantitative Proteomics, and Inferred Metalloproteomes.Environmental science & technology · 2025Article
- Coenzyme-protein interactions since early life.eLife · 2025Article
- Exploring Metalloproteome Remodeling in Calprotectin-StressedACS chemical biology · 2025Article
- Reconstructing biological molecules with help from video gamers.Acta crystallographica. Section D, Structural biology · 2025Article
- A bioinformatics approach to design minimal biomimetic metal-binding peptides.Communications chemistry · 2025Article
64 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
MetalPDB (http://metalweb.cerm.unifi.it/) is a database providing information on metal-binding sites detected in the three-dimensional (3D) structures of biological macromolecules. MetalPDB represents such sites as 3D templates, called Minimal Functional Sites (MFSs), which describe the local environment around the metal(s) independently of the larger context of the macromolecular structure. The 2018 update of MetalPDB includes new contents and tools. A major extension is the inclusion of proteins whose structures do not contain metal ions although their sequences potentially contain a known MFS. In addition, MetalPDB now provides extensive statistical analyses addressing several aspects of general metal usage within the PDB, across protein families and in catalysis. Users can also query MetalPDB to extract statistical information on structural aspects associated with individual metals, such as preferred coordination geometries or aminoacidic environment. A further major improvement is the functional annotation of MFSs; the annotation is manually performed via a password-protected annotator interface. At present, ∼50% of all MFSs have such a functional annotation. Other noteworthy improvements are bulk query functionality, through the upload of a list of PDB identifiers, and ftp access to MetalPDB contents, allowing users to carry out in-depth analyses on their own computational infrastructure.
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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.