MetalPDB
Names
More detailed information about this field from each metasource.
MetalPDB
metasource: Fairsharing.org
version: FAIRsharing.org: MetalPDB; MetalPDB; DOI: https://doi.org/10.25504/FAIRsharing.g646hq; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:12.957097
metalpdb
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:12.957097
Names
More detailed information about this field from each metasource.
MetalPDB
metasource: Fairsharing.orgversion: FAIRsharing.org: MetalPDB; MetalPDB; DOI: https://doi.org/10.25504/FAIRsharing.g646hq; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:12.957097
metalpdb
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:12.957097
Names
More detailed information about this field from each metasource.
MetalPDB
metasource: Fairsharing.orgversion: FAIRsharing.org: MetalPDB; MetalPDB; DOI: https://doi.org/10.25504/FAIRsharing.g646hq; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:12.957097
metalpdb
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:12.957097
MetalPDB is a resource aimed at conveying the information available on the three-dimensional 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 three-dimensional 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 analyze similarities and variations in metal-macromolecule interactions, and to link them to functional information.
Description
More detailed information about this field from each metasource.
MetalPDB is a resource aimed at conveying the information available on the three-dimensional 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 three-dimensional 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 analyze similarities and variations in metal-macromolecule interactions, and to link them to functional information.
metasource: Fairsharing.orgversion: FAIRsharing.org: MetalPDB; MetalPDB; DOI: https://doi.org/10.25504/FAIRsharing.g646hq; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
MetalPDB is a resource aimed at conveying the information available on the three-dimensional 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 three-dimensional 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 analyze 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. The Search menu of the interface offers various options to interrogate the database, including (i) by PDB code, (ii) by EC Number, (iii) by macromolecule name, (iv) by UniProt id, (v) by metal element, (vi) by performing a BLAST search, and (vii) through an Advanced Query interface. The latter allows users to formulate queries with varying degrees of complexity, by specifying e.g. molecule type (protein, nucleic acid, …), site nuclearity, metal contents, metal geometry. The various conditions set are connected by logical AND operators. Furthermore, the Advanced Query interface allows the results of a query to be downloaded to a file rather than visualized (which is instead the only option available for simple queries). MetalPDB is updated monthly in an automated manner.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Knowledge on metal sites in biological macromolecules, built on structural information in the Protein Data Bank (PDB).
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:12.957097
Webpage:
http://metalweb.cerm.unifi.it/Webpage
More detailed information about this field from each metasource.
http://metalweb.cerm.unifi.it/
metasource: Fairsharing.orgversion: FAIRsharing.org: MetalPDB; MetalPDB; DOI: https://doi.org/10.25504/FAIRsharing.g646hq; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:12.957097
Publications:
Publications
More detailed information about this field from each metasource.
MetalPDB: a database of metal sites in biological macromolecular structures
PMID: 23155064
metasource: Fairsharing.org
version: FAIRsharing.org: MetalPDB; MetalPDB; DOI: https://doi.org/10.25504/FAIRsharing.g646hq; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
http://dx.doi.org/10.1093/nar/gks1063
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:12.957097
Publications
More detailed information about this field from each metasource.
MetalPDB: a database of metal sites in biological macromolecular structures
PMID: 23155064
metasource: Fairsharing.org
version: FAIRsharing.org: MetalPDB; MetalPDB; DOI: https://doi.org/10.25504/FAIRsharing.g646hq; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
http://dx.doi.org/10.1093/nar/gks1063
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:12.957097
-
MetalPDB: a database of metal sites in biological macromolecular structures
PubMed citations: 46.
46 articles citing: MetalPDB: a database of metal sites in biological macromolecular structures
Structural Bioinformatics and Deep Learning of Metalloproteins: Recent Advances and Applications. PMID:35887033
The zinc proteome of SARS-CoV-2. PMID:35767875
Learning to Identify Physiological and Adventitious Metal-Binding Sites in the Three-Dimensional Structures of Proteins by Following the Hints of a Deep Neural Network. PMID:35679182
Role of water-bridged interactions in metal ion coupled protein allostery. PMID:35653400
mebipred: identifying metal binding potential in protein sequence. PMID:35639953
A Comprehensive Review of Computation-Based Metal-Binding Prediction Approaches at the Residue Level. PMID:35402609
Ten things I `hate' about refinement. PMID:34866607
Zn-Induced Interactions Between SARS-CoV-2 orf7a and BST2/Tetherin. PMID:34791819
virusMED: an atlas of hotspots of viral proteins. PMID:34614039
Comparative Genomic Analysis of the DUF34 Protein Family Suggests Role as a Metal Ion Chaperone or Insertase. PMID:34572495
Nitrite reductase activity within an antiparallel de novo scaffold. PMID:34487215
Structural Biology in the Clouds: The WeNMR-EOSC Ecosystem. PMID:34395534
AncPhore: A versatile tool for anchor pharmacophore steered drug discovery with applications in discovery of new inhibitors targeting metallo-β-lactamases and indoleamine/tryptophan 2,3-dioxygenases. PMID:34386329
InterMetalDB: A Database and Browser of Intermolecular Metal Binding Sites in Macromolecules with Structural Information. PMID:33502860
High-throughput mutagenesis reveals unique structural features of human ADAR1. PMID:33046702
Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes. PMID:32349661
SrnR from Streptomyces griseus is a nickel-binding transcriptional activator. PMID:31853648
Zinc binding proteome of a phytopathogen Xanthomonas translucens pv. undulosa. PMID:31598288
Catalytic Cycle of Neisseria meningitidis CMP-Sialic Acid Synthetase Illustrated by High-Resolution Protein Crystallography. PMID:31583886
Simple Coordination Geometry Descriptors Allow to Accurately Predict Metal-Binding Sites in Proteins. PMID:31459585
Methylated Histidines Alter Tautomeric Preferences that Influence the Rates of Cu Nitrite Reductase Catalysis in Designed Peptides. PMID:30983335
High-resolution archaellum structure reveals a conserved metal-binding site. PMID:30898768
Zinc regulates ERp44-dependent protein quality control in the early secretory pathway. PMID:30723194
ZincBind-the database of zinc binding sites. PMID:30722040
Design of metalloproteins and novel protein folds using variational autoencoders. PMID:30385875
Development of de Novo Copper Nitrite Reductases: Where We Are and Where We Need To Go. PMID:30294504
In silico Study of Iron, Zinc and Copper Binding Proteins of Pseudomonas syringae pv. lapsa: Emphasis on Secreted Metalloproteins. PMID:30186242
Assigning crystallographic electron densities with free energy calculations-The case of the fluoride channel Fluc. PMID:29771936
IDPM: an online database for ion distribution in protein molecules. PMID:29548284
To what extent do structural changes in catalytic metal sites affect enzyme function? PMID:29161638
MetalPDB in 2018: a database of metal sites in biological macromolecular structures. PMID:29077942
The Metal Drives the Chemistry: Dual Functions of Acireductone Dioxygenase. PMID:28731690
Microbial Metalloproteomics. PMID:28248278
Perspectives and expectations in structural bioinformatics of metalloproteins. PMID:28168746
Computational approaches for de novo design and redesign of metal-binding sites on proteins. PMID:28167677
Aberrant coordination geometries discovered in the most abundant metalloproteins. PMID:28142195
Cadmium(II) inhibition of human uracil-DNA glycosylase by catalytic water supplantation. PMID:27974818
Validation and correction of Zn-CysxHisy complexes. PMID:27710932
Minimal Functional Sites in Metalloproteins and Their Usage in Structural Bioinformatics. PMID:27153067
Quantifying Integrated Proteomic Responses to Iron Stress in the Globally Important Marine Diazotroph Trichodesmium. PMID:26562022
A less-biased analysis of metalloproteins reveals novel zinc coordination geometries. PMID:26009987
Hidden relationships between metalloproteins unveiled by structural comparison of their metal sites. PMID:25820752
Magnesium-binding architectures in RNA crystal structures: validation, binding preferences, classification and motif detection. PMID:25800744
MetalS(3), a database-mining tool for the identification of structurally similar metal sites. PMID:24699831
Cloning and characterization of a wheat homologue of apurinic/apyrimidinic endonuclease Ape1L. PMID:24667595
Validation of metal-binding sites in macromolecular structures with the CheckMyMetal web server. PMID:24356774 - http://dx.doi.org/10.1093/nar/gks1063
Tags:
Tags
More detailed information about this field from each metasource.
metal ion binding
metasource: Fairsharing.org
version: FAIRsharing.org: MetalPDB; MetalPDB; DOI: https://doi.org/10.25504/FAIRsharing.g646hq; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
protein structure
metasource: Fairsharing.org
version: FAIRsharing.org: MetalPDB; MetalPDB; DOI: https://doi.org/10.25504/FAIRsharing.g646hq; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
structure
metasource: Fairsharing.org
version: FAIRsharing.org: MetalPDB; MetalPDB; DOI: https://doi.org/10.25504/FAIRsharing.g646hq; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
structure databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
nucleic acid structure
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
biochemistry
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:12.957097
Tags
More detailed information about this field from each metasource.
metal ion binding
metasource: Fairsharing.orgversion: FAIRsharing.org: MetalPDB; MetalPDB; DOI: https://doi.org/10.25504/FAIRsharing.g646hq; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
protein structure
metasource: Fairsharing.orgversion: FAIRsharing.org: MetalPDB; MetalPDB; DOI: https://doi.org/10.25504/FAIRsharing.g646hq; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
structure
metasource: Fairsharing.orgversion: FAIRsharing.org: MetalPDB; MetalPDB; DOI: https://doi.org/10.25504/FAIRsharing.g646hq; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
structure databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
nucleic acid structure
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
biochemistry
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:36:12.957097
metal ion binding protein structure structure structure nucleic acid structure biochemistry
Need help integrating and/or managing biomedical data?