Pregled bibliografske jedinice broj: 586566
BioMe : biologically relevant metals
BioMe : biologically relevant metals // Nucleic acids research, 40 (2012), W352-W357 doi:10.1093/nar/gks514 (međunarodna recenzija, članak, znanstveni)
CROSBI ID: 586566 Za ispravke kontaktirajte CROSBI podršku putem web obrasca
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
Projekti:
022-0222148-2822 - Modeliranje i međudjelovanje kompleksa prijelaznih metala i bioliganada (Sabolović, Jasmina, MZOS ) ( CroRIS)
036-0362214-1987 - Modeliranje kompleksnih sustava (Jeren, Branko, MZO ) ( CroRIS)
098-1191344-2860 - Proučavanje biomakromolekula računalnim metodama i razvoj novih algoritama (Tomić, Sanja, MZOS ) ( CroRIS)
Ustanove:
Institut za medicinska istraživanja i medicinu rada, Zagreb,
Fakultet elektrotehnike i računarstva, Zagreb,
Institut "Ruđer Bošković", Zagreb
Citiraj ovu publikaciju:
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