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FindGeo specifications

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Unique identifier OMICS_07660
Name FindGeo
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Claudia Andreini <>

Information


Unique identifier OMICS_07660
Name FindGeo
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Claudia Andreini <>

Publication for FindGeo

FindGeo citations

 (4)
library_books

Transition metal binding selectivity in proteins and its correlation with the phylogenomic classification of the cation diffusion facilitator protein family

2017
PMCID: 5703985
PMID: 29180655
DOI: 10.1038/s41598-017-16777-5

[…] specific metal cations (total number of bonds to all of the residues’ atoms from all used metals). coordination geometries for all metals considered were calculated by the stand-alone version of the findgeo server in its default settings. findgeo accepts the metal and coordination ligands (a pdb file) as an input. the output is the most probable geometry for metal coordination from a library […]

library_books

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

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

[…] [] combine information from both protein sequence and structure. use of ab initio methods as in ioncom [] server has also been recently realized. several helper tools such as metals2 [], metals3 [], findgeo [], checkmymetal (cmm) [] were developed for pairwise structural alignment, database mining of metal-binding sites, determination of metal co-ordination geometry, validation of metal-binding […]

library_books

Calcium binding by the PKD1 domain regulates interdomain flexibility in Vibrio cholerae metalloprotease PrtV☆

2013
PMCID: 3722578
PMID: 23905008
DOI: 10.1016/j.fob.2013.06.003

[…] the ca2+ ion binds to four carboxylate atoms from a conserved acidic motif and to one water molecule (a and b). the coordination sphere of the five-ligand-coordinated ca2+ ion is irregular (findgeo server []). this is not uncommon as calcium-binding sites in proteins in general are highly irregular with large variation in ligand type, length, and angle of the metal coordination shell […]

library_books

Minimal Functional Sites Allow a Classification of Zinc Sites in Proteins

2011
PMCID: 3197139
PMID: 22043316
DOI: 10.1371/journal.pone.0026325

[…] of the zinc ligands). this set was used to analyse the coordination sphere of zinc sites as described in . the coordination geometry of four-coordinated zinc ions in this set was calculated by findgeo, an in-house developed tool that automatically determines the best-fit geometry among a number of possible ideal geometries. the representative zinc sites were compared against one another […]


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FindGeo institution(s)
Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy

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