Algoritmi za utvrđivanje fleksibilnosti proteina na temelju konformacije i fizikalnih svojstava proteina

doctoral thesis

• Title (english): Algorithms for determination of protein flexibility based on conformations and physical properties of protein
• Author: Krešimir Šikić
• Mentor: Branko Jeren (mentor)
• Mentor: Sanja Tomić (komentor)
• Committee member: Sven Lončarić (član povjerenstva)
• Committee member: Branko Jeren (član povjerenstva)
• Committee member: Sanja Tomić (član povjerenstva)
• Committee member: Mladen Kos (član povjerenstva)
• Committee member: Davor Petrinović (član povjerenstva)
• Granter: University of Zagreb; Faculty of Electrical Engineering and Computing; (Department of Electronic Systems and Information Processing); Zagreb
• Granter: Ruđer Bošković Institute; Zagreb
• Defense date and country: 2008-09-29, Croatia
• Scientific / art field, discipline and subdiscipline: TECHNICAL SCIENCES; Electrical Engineering; Electronics
• Scientific / art field, discipline and subdiscipline: TECHNICAL SCIENCES; Computing; Data Processing
• Scientific / art field, discipline and subdiscipline: INTERDISCIPLINARY AREAS OF KNOWLEDGE; Biotechnology in Biomedicine (natural science, biomedicine and healthcare, bioethics area
• Universal decimal classification (UDC): 621.3; APPLIED SCIENCES. MEDICINE. TECHNOLOGY; Electrical engineering
• Universal decimal classification (UDC): 60; APPLIED SCIENCES. MEDICINE. TECHNOLOGY; Biotechnology. Genetic engineering. Products of cloning

Abstract

Tema ovog rada je proučavanje fleksibilnosti proteina. U cilju proučavanja fleksibilnosti proteina u radu su predložene dvije nove metode za utvrđivanje fleksibilnosti. Metode su apriori i aposteriori. Prva metoda identificira fleksibilne i rigidne domene u proteinu na temelju karakteristika jednog prostornog oblika korištenjem kompleksnih modela i aproksimacija. Druga metoda se temelji na usporedbi dvaju prostornih oblika istog proteina. Prva metoda je točnija iz razloga što uzima u razmatranje dva prostorna oblika, ali nije uvijek upotrebljiva. Druga metoda se može uvijek primijeniti jer zahtijeva samo jedan prostorni oblik. Usporedbom rezultata dobivenih korištenjem ovih metoda dokazano je da je apriori dovoljno točna kako bi se mogla koristiti u budućim istraživanjima. Temeljem apostreriori metode napravljen je testni skup koji je moguće koristiti za testiranje novih metoda za određivanje fleksibilnosti. Kako obradba informacija u ovom radu ovisi o PDB zapisima napravljena je i sveobuhvatna usporedba PDB zapisa dobivenih različitim tehnikama. Na ovaj način su utvrđene razlike u zapisima koje mogu utjecati na istraživanja.

Abstract (english)

This thesis is focused on studying protein flexibility. For that purpose two new methods for protein flexibility identification based on information processing have been proposed. Methods are named apriori and aposteriori. First method identifies flexible and rigid domains in protein on a basis of single conformation properties using complex models and approximations. Second method relies on comparison of two conformations of the same protein. However, I consider first method to be more accurate one but due to its limitations (two conformations required) it is not always applicable, while second method requiring only one conformation can always be applied. By comparing results obtained with these methods I have proofed that the accuracy of the apriori is high enough to be use in future studies. Also using proposed aposteriori a limited size benchmark for the purpose of developing future methods has been created. As information processing in this thesis relies on PDB entries a large scale comparison between different types of entries has been done in order to determine differences and possible pitfalls in the research.

• Keywords: fleksibilnost; protein; obradba informacija; kompleksni sustav; poravnavanje; analiza normalnog moda; apriori metoda; aposteriori metoda; protein data bank (PDB); razredovanje
• Keywords (english): flexibility; protein; information processing; complex system; alignment; normal mode analysis; apriori method; aposteriori method; protein data bank (PDB); clustering
• Language: croatian
• URN:NBN: urn:nbn:hr:168:483110
• Study programme: Title: Electrical Engineering and Computing; Study programme type: university; Study level: postgraduate; Academic / professional title: Doktor znanosti elektrotehnike i računarstva (Doktor znanosti elektrotehnike i računarstva)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Closed access
• Created on: 2020-05-26 06:24:20