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BioMe : biologically relevant metals


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 (međunarodna recenzija, članak, znanstveni)


Naslov
BioMe : biologically relevant metals

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

Izvornik
Nucleic acids research (0305-1048) 40 (2012); W352-W357

Vrsta, podvrsta i kategorija rada
Radovi u časopisima, članak, znanstveni

Ključne riječi
Metals; proteins; nucleic acids; web server; database

Sažetak
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.

Izvorni jezik
Engleski

Znanstvena područja
Kemija, Biologija, Računarstvo



POVEZANOST RADA


Projekt / tema
022-0222148-2822 - Modeliranje i međudjelovanje kompleksa prijelaznih metala i bioliganada (Jasmina Sabolović, )
036-0362214-1987 - Modeliranje kompleksnih sustava (Branko Jeren, )
098-1191344-2860 - Proučavanje biomakromolekula računalnim metodama i razvoj novih algoritama (Sanja Tomić, )

Ustanove
Institut za medicinska istraživanja i medicinu rada, Zagreb,
Fakultet elektrotehnike i računarstva, Zagreb,
Institut "Ruđer Bošković", Zagreb

Časopis indeksira:


  • Current Contents Connect (CCC)
  • Web of Science Core Collection (WoSCC)
    • Science Citation Index Expanded (SCI-EXP)
    • SCI-EXP, SSCI i/ili A&HCI
  • Scopus
  • MEDLINE


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