Database Commons

a catalog of biological databases

e.g., animal; RNA; Methylation; China

Database Profile

General information

URL: https://intermetaldb.biotech.uni.wroc.pl
Full name:
Description: InterMetalDB automatically aggregates and allows easy access to the intermolecular metal sites in biological macromolecules with structural information deposited in Protein Data Bank (PDB).
Year founded: 2020
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Country/Region: Poland
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Contact information

University/Institution: University of Wrocław
Address: Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, 50-383 Wrocław, Poland.
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Country/Region: Poland
Contact name (PI/Team): Artur Krężel
Contact email (PI/Helpdesk): artur.krezel@uwr.edu.pl

Publications

33502860
InterMetalDB: A Database and Browser of Intermolecular Metal Binding Sites in Macromolecules with Structural Information. [PMID: 33502860]
Józef Ba Tran, Artur Krężel

InterMetalDB is a free-of-charge database and browser of intermolecular metal binding sites that are present on the interfaces of macromolecules forming larger assemblies based on structural information deposited in Protein Data Bank (PDB). It can be found and freely used at https://intermetaldb.biotech.uni.wroc.pl/. InterMetalDB collects the interfacial binding sites with involvement of metal ions and clusters them on the basis of 50% sequence similarity and the nearest metal environment (5 Å radius). The data are available through the web interface where they can be queried, viewed, and downloaded. Complexity of the query depends on the user, because the questions in the query are connected with each other by a logical AND. InterMetalDB offers several useful options for filtering records including searching for structures by particular parameters such as structure resolution, structure description, and date of deposition. Records can be filtered by coordinated metal ion, number of bound amino acid residues, coordination sphere, and other features. InterMetalDB is regularly updated and will continue to be regularly updated with new content in the future. InterMetalDB is a useful tool for all researchers interested in metalloproteins, protein engineering, and metal-driven oligomerization.

J Proteome Res. 2021:() | 0 Citations (from Europe PMC, 2021-05-01)

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Created on: 2021-03-10
Curated by:
lin liu [2021-03-25]
Dong Zou [2021-03-10]