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MetalDetector specifications

Information


Unique identifier OMICS_12271
Name MetalDetector
Interface Web user interface
Restrictions to use None
Input data An amino acid sequence.
Input format The input sequence can be entered either as a plain amino acid string or in FASTA format.
Output data It consists of a table having an entry for each CYS and HIS, with the indication of its position within the sequence, its predicted bonding state and, if the residue was predicted as metal bonded, the assigned metal ion identifier.
Computer skills Basic
Version 2.0
Stability Stable
Maintained Yes

Information


Unique identifier OMICS_12271
Name MetalDetector
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes

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Publications for MetalDetector

MetalDetector citations

 (9)
library_books

Biochemical characterization of functional domains of the chaperone Cosmc

2017
PLoS One
PMCID: 5493369
PMID: 28665962
DOI: 10.1371/journal.pone.0180242

[…] lkylated the protein; alkylation did not affect its metal binding activity by thermal shift assays. Bioinformatics prediction servers based on protein sequence (ZincPred, MetalPredator, ZincExplorer, MetalDetector v2.0) yielded ambiguous results regarding the residues that might be directly involved in metal chelation.In order to identify whether endogenous metals are bound in recombinantly purifi […]

library_books

Computational approaches for de novo design and redesign of metal binding sites on proteins

2017
Biosci Rep
PMCID: 5482196
PMID: 28167677
DOI: 10.1042/BSR20160179

[…] ifs are then used to search for similar patterns in newly identified proteins. Machine learning methods have also been introduced to the problem only recently [,–]. Programs such as MetalPredator [], MetalDetector v2.0 [], SeqCHED Server [], ZincFinder [], SVMProt [,] employ sequence based approaches for the prediction of the metal ion-binding sites. For instance MetalDetector v2.0 [] uses cystein […]

library_books

The Lifestyle Switch Protein Bd0108 of Bdellovibrio bacteriovorus Is an Intrinsically Disordered Protein

2014
PLoS One
PMCID: 4267844
PMID: 25514156
DOI: 10.1371/journal.pone.0115390

[…] hydration 18.6 kDa) with low polydispersity, indicating that the small species is mono-disperse and is likely not in equilibrium with the larger species.Given that Bd0108 has a predicted disulfide by Metaldetector (), we hypothesized that the larger species may be a result of improper disulfide formation during over-expression and/or concentration. To test this, we ran an SDS-PAGE gel of Bd0108 t […]

library_books

A Sco protein among the hypothetical proteins of Bacillus lehensis G1: Its 3D macromolecular structure and association with Cytochrome C Oxidase

2014
BMC Struct Biol
PMCID: 3994876
PMID: 24641837
DOI: 10.1186/1472-6807-14-11

[…] e possible presence of consensus amino acids pattern in Bleg1_2507 sequence was identified using ScanProsite []. Important and metal-binding residues were subsequently identified using Consurf [] and MetalDetector v 2.0 [] respectively. The physicochemical aspect of the protein such as its theoretical pI value was investigated using ProtParam []. SigCleave from EMBOSS [] was used to investigate th […]

library_books

Secondary Structure Preferences of Mn2+ Binding Sites in Bacterial Proteins

2014
Adv Bioinformatics
PMCID: 3977119
PMID: 24778647
DOI: 10.1155/2014/501841

[…] d Mn2+ than glutamic acid and histidine.Information on amino acid preferences and geometry of coordination spheres is used in algorithms for metal binding sites prediction, such as FINDSITE-metal [], MetalDetector v2.0 [], Fold-X [], and FlexX []. However, the information on preferable 3D structural motifs is available mostly for Ca2+ and Zn2+ binding proteins. Well-known EF-hand motif for Ca2+ bi […]

library_books

Powerful Sequence Similarity Search Methods and In Depth Manual Analyses Can Identify Remote Homologs in Many Apparently “Orphan” Viral Proteins

2014
J Virol
PMCID: 3911697
PMID: 24155369
DOI: 10.1128/JVI.02595-13

[…] ces of CBPV and negeviruses corresponds to 50 aa in the N-terminal or central part of ORF2, which contains nine conserved residues, including four cysteines (), predicted to form disulfide bridges by Metaldetector (). Outside of this region, we could detect no further sequence or secondary-structure similarity between ORF2 of CBPV and that of negeviruses. However, they are similar in organization, […]


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MetalDetector institution(s)
Dipartimento di Ingegneria e Scienza dell'Informazione, Università degli Studi di Trento, Povo di Trento, Italy; Dipartimento di Sistemi e Informatica, Università degli Studi di Firenze, Firenze, Italy

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