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|9 34711
|a Tus, Alan
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|a BioMe - alat za statističku analizu viološki važnih metala :
|b [nagrađeni studentski rad za Rektorovu nagradu u ak.god. 2011./2012.]
|c mentor Mile Šikić
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|a Zagreb :
|b Fakultet elektrotehnike i računarstva,
|c 2012.
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|a vi, 53 str. :
|b ilustr. u bojama ;
|c 30 cm.
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|a U ovom radu je opisan sustav za statistiˇcku analizu metala u biomolekulama izra
¯ den na Fakultetu elektrotehnike i raˇcunarstva na Sveuˇcilištu u Zagrebu. Sustav se sastoji od tri dijela: baze podataka, parsera i web suˇcelja za statistiˇcku analizu. Potpuno je automatiziran te se osvježava svakog tjedna nakon ažuriranja centralne proteinske baze podataka (http://www.pdb.org/) iz koje se preuzimaju podaci. Razvoj traje ve´ c tre´cu godinu i u planu su još mnoge nadogradnje i proširenja. Višedretveni parser mmCIF datoteka je implementiran u Java tehnologiji i optimiziran tako da iskoristi prednosti višeprocesorskog okruženja. Obavlja posao odabira, analize i spremanja odabranih struktura iz oko 16 GB ulaznih podataka. mySQL baza podataka u konaˇcnici sadrži podatke o svim strukturama, lancima, metalnim ligandima i atomima te odgovaraju´cim udaljenostima, kutovima i geometrijskim strukturama. Takostvorenabazapodataka,veliˇcineoko150MB,služizastatistiˇckuanalizui javnojedostupnazapreuzimanje. Prvenstvenosudostupnipodacizaproteinske,RNA i DNA lance, ali i za sve ostale komponente biomolekula. Statistiˇcku analizu mogu´ce je obaviti kroz web suˇcelje implementirano pomo´cu GWT-a. Korisnik može saznati razne statistiˇcke podatke kao što su prisustvo odabranog liganda u koordinaciji s metalom, raspodjelu koordinacijski brojeva, postotak metalnih iona koordiniran s kombinacijama odabranih ligada, raspodjelu monodentatnih i bidentatnih metalnih karboksila, raspodjelu po koordinatnim geometrijama te druge. Rezultati su dostupni u brojevnom i grafiˇckom formatu. Baza podataka i suˇcelje za statistiˇcku analizu služe kao bogat izvor informacija za istraživaˇcku zajednicu. Uloga metala u proteinima je još uvijek slabo istraženo podruˇ cje,stogavjerujemoda ´ceovajalatposlužitiznanstvenicimaubudu´cimistraživanjima. U usporedbi s postoje´cim alatima, ovaj alat je daleko nadmo´cniji zato što uvijek nudi najsvježiju informaciju, objedinjuje sve ponu¯dene podatke na jednom mjestu i nudi mnoštvo novih podataka. Osim navedenoga, sustav je brži i stabilniji. Dostupan je na http://metals.zesoi.fer.hr.
Kljuˇcnerijeˇci: PDB, proteini, nukeinske kiseline, biometali, statistiˇcka analiza
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|a This paper offers an overview of the statistical analyzer for biometals which was developed at the Faculty of Electrical Engineering and Computing at the University of Zagreb, Croatia. The system consists of three parts: a database, file parser and web interfaceforstatisticalanalysis. Itiscompletelyautomated,soitdoesaweeklyrefresh after the update of the central Protein Data Bank (http://www.pdb.org/), which is also our main data source. The system has been in development for almost 3 years and many further upgrades and expansions are yet to come. Themulti-threadedmmCIFfileparserisimplementedinJavatechnologyandoptimizedsothatitutilizesthemultiprocessorenvironment. Itselectsandanalysesapprox. 16 GB of structures and then stores the ones which fulfill the predetermined criteria into a database. The resulting mySQL database (approx. 150 MB) contains information about all selected structures, chains, residues and corresponding distances, angles and geometric structures. This database is later used for statistical analysis and it is publiclyavailablefordownload. Dataaboutprotein,DNAandRNAchainsaremainly available as well as data about other components of the biomolecule. Statistical analysis is carried out using a web based interface implemented using GWT.Userscanobtainthefollowingstatisticalproperties: presenceofselectedligands inametalcoordinationsphere,distributionofcoordinationnumbers,thepercentageof metal ions coordinated by the combination of the selected ligands, the distribution of monodentate and bidentate metal-carboxyl, the distribution of coordination geometry and others. The database and statistical analysis interface can be used as a rich source of information for the scientific community. The role of metals in proteins is still an area where very little research has been carried out, so we believe this tool will be of use to researchers. In comparison with other available tools, this tool is better since it always offers up-to-date information, consolidates all the information in one place and offers a broad variety of new details. Additionally, the system is faster and more stable. It is available at http://metals.zesoi.fer.hr.
Keywords: PDB, proteins, nucleic acids, biometals, statistical analysis
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|a Rakipović, Alen
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