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InterMetalDB: A Database and Browser of Intermolecular Metal Binding Sites in Macromolecules with Structural Information

[Image: see text] 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:...

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Autores principales: Tran, Józef Ba, Krężel, Artur
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Chemical Society 2021
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8023803/
https://www.ncbi.nlm.nih.gov/pubmed/33502860
http://dx.doi.org/10.1021/acs.jproteome.0c00906
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author Tran, Józef Ba
Krężel, Artur
author_facet Tran, Józef Ba
Krężel, Artur
author_sort Tran, Józef Ba
collection PubMed
description [Image: see text] 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.
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spelling pubmed-80238032021-04-07 InterMetalDB: A Database and Browser of Intermolecular Metal Binding Sites in Macromolecules with Structural Information Tran, Józef Ba Krężel, Artur J Proteome Res [Image: see text] 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. American Chemical Society 2021-01-27 2021-04-02 /pmc/articles/PMC8023803/ /pubmed/33502860 http://dx.doi.org/10.1021/acs.jproteome.0c00906 Text en © 2021 The Authors. Published by American Chemical Society This is an open access article published under a Creative Commons Attribution (CC-BY) License (https://pubs.acs.org/page/policy/authorchoice_ccby_termsofuse.html) , which permits unrestricted use, distribution and reproduction in any medium, provided the author and source are cited.
spellingShingle Tran, Józef Ba
Krężel, Artur
InterMetalDB: A Database and Browser of Intermolecular Metal Binding Sites in Macromolecules with Structural Information
title InterMetalDB: A Database and Browser of Intermolecular Metal Binding Sites in Macromolecules with Structural Information
title_full InterMetalDB: A Database and Browser of Intermolecular Metal Binding Sites in Macromolecules with Structural Information
title_fullStr InterMetalDB: A Database and Browser of Intermolecular Metal Binding Sites in Macromolecules with Structural Information
title_full_unstemmed InterMetalDB: A Database and Browser of Intermolecular Metal Binding Sites in Macromolecules with Structural Information
title_short InterMetalDB: A Database and Browser of Intermolecular Metal Binding Sites in Macromolecules with Structural Information
title_sort intermetaldb: a database and browser of intermolecular metal binding sites in macromolecules with structural information
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8023803/
https://www.ncbi.nlm.nih.gov/pubmed/33502860
http://dx.doi.org/10.1021/acs.jproteome.0c00906
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