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izvor podataka: crosbi

BioMe : biologically relevant metals (CROSBI ID 185101)

Prilog u časopisu | izvorni znanstveni rad | međunarodna recenzija

Tus, Alan ; Rakipović, Alen ; Peretin, Goran ; Tomić, Sanja ; Šikić, Mile BioMe : biologically relevant metals // Nucleic acids research, 40 (2012), W352-W357. doi: 10.1093/nar/gks514

Podaci o odgovornosti

Tus, Alan ; Rakipović, Alen ; Peretin, Goran ; Tomić, Sanja ; Šikić, Mile

engleski

BioMe : biologically relevant metals

In this article, we introduce BioMe (biologically relevant metals), a web-based platform for calculation of various statistical properties of metal-binding sites. Users can obtain the following statistical properties: presence of selected ligands in metal coordination sphere, distribution of coordination numbers, percentage of metal ions coordinated by the combination of selected ligands, distribution of monodentate and bidentate metal-carboxyl, bindings for ASP and GLU, percentage of particular binuclear metal centers, distribution of coordination geometry, descriptive statistics for a metal ion–donor distance and percentage of the selected metal ions coordinated by each of the selected ligands. Statistics is presented in numerical and graphical forms. The underlying database contains information about all contacts within the range of 3 Å from a metal ion found in the asymmetric crystal unit. The stored information for each metal ion includes Protein Data Bank code, structure determination method, types of metal- binding chains [protein, ribonucleic acid (RNA), deoxyribonucleic acid (DNA), water and other] and names of the bounded ligands (amino acid residue, RNA nucleotide, DNA nucleotide, water and other) and the coordination number, the coordination geometry and, if applicable, another metal(s). BioMe is on a regular weekly update schedule. It is accessible at http://metals.zesoi.fer.hr.

metals; proteins; nucleic acids; web server; database

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Podaci o izdanju

40

2012.

W352-W357

objavljeno

0305-1048

10.1093/nar/gks514

Povezanost rada

Kemija, Računarstvo, Biologija

Poveznice
Indeksiranost