Приказ основних података о дисертацији
Prediction of alphabets of local protein structures using data mining methods: doctoral dissertation
Predviđanje alfabeta lokalne strukture proteina primenom metoda istraživanja podataka
dc.contributor.advisor | Mitić, Nenad | |
dc.contributor.other | Malkov, Saša | |
dc.contributor.other | Kovačević, Jovana | |
dc.contributor.other | de Brevern, Alexandre | |
dc.creator | Maljković, Mirjana M. | |
dc.date.accessioned | 2023-09-06T11:00:08Z | |
dc.date.available | 2023-09-06T11:00:08Z | |
dc.date.issued | 2019-10-15 | |
dc.identifier.uri | https://uvidok.rcub.bg.ac.rs/bitstream/handle/123456789/4499/Referat.pdf | |
dc.identifier.uri | https://eteze.bg.ac.rs/application/showtheses?thesesId=9178 | |
dc.identifier.uri | https://fedorabg.bg.ac.rs/fedora/get/o:30500/bdef:Content/download | |
dc.identifier.uri | https://plus.cobiss.net/cobiss/sr/sr/bib/121633289 | |
dc.identifier.uri | https://nardus.mpn.gov.rs/handle/123456789/21558 | |
dc.description.abstract | Proteins are linear biological polymers composed of amino acids whose structure and function are determined by the number and order of amino acids. The structure of the protein has three levels: primary, secondary and ter- tiary (three-dimensional, 3D) structure. Since the experimental determination of protein 3D structure is expensive and time-consuming, it is important to develop predictors of protein 3D structure properties from the amino acid sequence (pri- mary structure), such as 3D structure of the protein backbone. The 3D structure of the backbone can be described using prototypes of local protein structure, i.e. prototypes of protein fragments with a length of few amino acids. A set of local structure prototypes determines the library of local protein structures, also called the structural alphabet. A structural alphabet is defined as a set of N proto- types of L amino acid length. The subject of this dissertation is the development of models for the prediction of structural alphabet prototypes for a given amino acid sequence using different data mining approaches. As one of the most known, structural alphabet Protein Blocks (PBs) was used in one part of the doctorial re- search. Structural alphabet PBs consists of 16 prototypes that are defined using fragments of 5 consecutive amino acids. The amino acid sequence is combined with the structural properties of a protein that can be determined based on amino acid sequence (occurrence of repeats in the amino acid sequence) and results of predictors of protein structural properties (backbone angles, secondary structures, occurrence of disordered regions, accessible surface area of amino acids) as an input to the prediction model of structural alphabet prototypes. Besides the de- velopment of models for prediction of prototypes of existing structural alphabet, the analysis of the capability of developing new structural alphabets is researched by applying the TwoStep clustering algorithm and construction of models for the prediction of prototypes of new structural alphabets. Several structural alpha- bets, which differ in the length of prototypes and the number of prototypes, have been constructed and analyzed. Fragments of the large number of proteins, whose structure is experimentally determined, were used to construct the new structural alphabets. | sr |
dc.description.abstract | Proteini su linearni biološki polimeri sastavljeni od aminokiselina čiji broj i redosled određuju strukturu i funkciju proteina. Struktura proteina je defin- isana sa tri nivoa: primarnom, sekundarnom i tercijarnom (trodimenzionalnom, 3D) strukturom. Pošto je eksperimentalno određivanje 3D strukture proteina skupo i vremenski zahtevno, postoji potreba za razvojem programa koji na osnovu aminokiselinske sekvence (primarne strukture) predviđaju osobine 3D strukture, kao što je 3D struktura glavnog lanca proteina (eng. backbone). 3D struktura glavnog lanca proteina može da se opiše korišćenjem prototipova lokalne strukture proteina, tj. delova proteina od nekoliko uzastopnih aminokiselina. Skup defin- isanih prototipova lokalne strukture čini biblioteku lokalnih struktura proteina, koja se još naziva i strukturni alfabet (eng. structural alphabet). Svaki strukturni alfabet je definisan kao skup od N prototipova dužine L aminokiselina. Pred- met ove disertacije je pravljenje modela za predviđanje prototipova strukturnog alfabeta za zadatu aminokiselinsku sekvencu primenom različitih algoritama is- traživanja podataka. Kao jedan od najpoznatijih, strukturni alfabet Protenski blokovi (eng. Protein Blocks) je korišćen u jednom delu istraživanja u okviru dis- ertacije. Strukturni alfabet Proteinski blokovi se sastoji od 16 prototipova koji su napravljeni na osnovu delova proteina od 5 uzastopnih aminokiselina. Kao ulaz u model za predviđanje prototipova strukturnog alfabeta koriste se strukturne osobine proteina koje mogu da se odrede na osnovu aminokiselinske sekvence (lokacija ponavljajuće niske u aminokiselinskoj sekvenci) i rezultati predviđanja nekih strukturnih osobina proteina (uglovi glavnog lanca, sekundarne strukture, pojavljivanje neuređenih regiona, pristupačna površina). Pored razvoja modela za predviđanje prototipova postojećeg strukturnog alfabeta, u radu je izvršena i analiza mogućnosti razvoja novih strukturnih alfabeta primenom algoritma klas- terovanja TwoStep i pravljenje modela za predviđanje prototipova novih struk- turnih alfabeta. Radi analize, napravljeno je više strukturnih alfabeta sa različitim brojem prototipova i različite dužine prototipova. Za istraživanje novih strukturni alfabeta korišćeni su delovi velikog broja proteina čija je struktura eksperimen- talno određena | en |
dc.format | application/pdf | |
dc.language | sr | |
dc.publisher | Универзитет у Београду, Математички факултет | sr |
dc.rights | openAccess | en |
dc.rights.uri | https://creativecommons.org/licenses/by-nc-nd/4.0/ | |
dc.source | Универзитет у Београду | sr |
dc.subject | data mining | sr |
dc.subject | straživanje podataka | en |
dc.subject | structural alphabet | sr |
dc.subject | prediction model | sr |
dc.subject | Protein Blocks | sr |
dc.subject | strukturni alfabeti | en |
dc.subject | model za predviđanje | en |
dc.subject | Proteinski blokovi | en |
dc.title | Prediction of alphabets of local protein structures using data mining methods: doctoral dissertation | sr |
dc.title.alternative | Predviđanje alfabeta lokalne strukture proteina primenom metoda istraživanja podataka | en |
dc.type | doctoralThesis | |
dc.rights.license | BY-NC-ND | |
dc.identifier.fulltext | http://nardus.mpn.gov.rs/bitstream/id/151592/Disertacija_13640.pdf | |
dc.identifier.fulltext | http://nardus.mpn.gov.rs/bitstream/id/152519/Referat.pdf | |
dc.identifier.rcub | https://hdl.handle.net/21.15107/rcub_nardus_21558 |