ArticleJournal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry2014
MetalS(3), a database-mining tool for the identification of structurally similar metal sites.
Article in Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed.
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- COLLAPSE: A representation learning framework for identification and characterization of protein structural sites.Protein science : a publication of the Protein Society · 2023Article
- Biological Effects of Human Exposure to Environmental Cadmium.Biomolecules · 2022Review
- The zinc proteome of SARS-CoV-2.Metallomics : integrated biometal science · 2022Article
- Structural Bioinformatics and Deep Learning of Metalloproteins: Recent Advances and Applications.International journal of molecular sciences · 2022Review
- Structure and activity of a thermally stable mutant of Acanthamoeba actophorin.Acta crystallographica. Section F, Structural biology communications · 2022Article
- Identifying metal binding amino acids based on backbone geometries as a tool for metalloprotein engineering.Protein science : a publication of the Protein Society · 2021Article
- ProteinsPlus: interactive analysis of protein-ligand binding interfaces.Nucleic acids research · 2020Article
- Crystallographic characterization of a tri-Asp metal-binding site at the three-fold symmetry axis of LarE.Scientific reports · 2020Article
- Structure, function and evolution of the hemerythrin-like domain superfamily.Protein science : a publication of the Protein Society · 2018Article
- To what extent do structural changes in catalytic metal sites affect enzyme function?Journal of inorganic biochemistry · 2018Article
- MetalPDB in 2018: a database of metal sites in biological macromolecular structures.Nucleic acids research · 2018Article
- Computational approaches forBioscience reports · 2017Review
- Structural and functional characterization of a calcium-activated cation channel from Tsukamurella paurometabola.Nature communications · 2016Article
- Minimal Functional Sites in Metalloproteins and Their Usage in Structural Bioinformatics.International journal of molecular sciences · 2016Review
- Structural basis for misfolding in myocilin-associated glaucoma.Human molecular genetics · 2015Article
- Hidden relationships between metalloproteins unveiled by structural comparison of their metal sites.Scientific reports · 2015Article
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4 authors.
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Abstract
We have developed a database search tool to identify metal sites having structural similarity to a query metal site structure within the MetalPDB database of minimal functional sites (MFSs) contained in metal-binding biological macromolecules. MFSs describe the local environment around the metal(s) independently of the larger context of the macromolecular structure. Such a local environment has a determinant role in tuning the chemical reactivity of the metal, ultimately contributing to the functional properties of the whole system. The database search tool, which we called MetalS(3) (Metal Sites Similarity Search), can be accessed through a Web interface at http://metalweb.cerm.unifi.it/tools/metals3/ . MetalS(3) uses a suitably adapted version of an algorithm that we previously developed to systematically compare the structure of the query metal site with each MFS in MetalPDB. For each MFS, the best superposition is kept. All these superpositions are then ranked according to the MetalS(3) scoring function and are presented to the user in tabular form. The user can interact with the output Web page to visualize the structural alignment or the sequence alignment derived from it. Options to filter the results are available. Test calculations show that the MetalS(3) output correlates well with expectations from protein homology considerations. Furthermore, we describe some usage scenarios that highlight the usefulness of MetalS(3) to obtain mechanistic and functional hints regardless of homology.
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