prikaz prve stranice dokumenta Development of an extended amino acid hydrophobicity scale
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master's thesis
Development of an extended amino acid hydrophobicity scale
Split: University of Split, University of Split, Faculty of science, 2016. urn:nbn:hr:166:365242
Gujinović, Luka
University of Split
Faculty of Science
Department of Physics

Institutional repository: Repository of Faculty of Science

Cite this document

Gujinović, L. (2016). Development of an extended amino acid hydrophobicity scale (Master's thesis). Split: University of Split, Faculty of Science. Retrieved from https://urn.nsk.hr/urn:nbn:hr:166:365242

Gujinović, Luka. "Development of an extended amino acid hydrophobicity scale." Master's thesis, University of Split, Faculty of Science, 2016. https://urn.nsk.hr/urn:nbn:hr:166:365242

Gujinović, Luka. "Development of an extended amino acid hydrophobicity scale." Master's thesis, University of Split, Faculty of Science, 2016. https://urn.nsk.hr/urn:nbn:hr:166:365242

Gujinović, L. (2016). 'Development of an extended amino acid hydrophobicity scale', Master's thesis, University of Split, Faculty of Science, accessed 15 November 2024, https://urn.nsk.hr/urn:nbn:hr:166:365242

Gujinović L. Development of an extended amino acid hydrophobicity scale [Master's thesis]. Split: University of Split, Faculty of Science; 2016 [cited 2024 November 15] Available at: https://urn.nsk.hr/urn:nbn:hr:166:365242

L. Gujinović, "Development of an extended amino acid hydrophobicity scale", Master's thesis, University of Split, Faculty of Science, Split, 2016. Available at: https://urn.nsk.hr/urn:nbn:hr:166:365242

Metadata
TitleDevelopment of an extended amino acid hydrophobicity scale
Title (croatian)Konstrukcija proširene ljestvice hidrofobnosti aminokiselina
AuthorLuka Gujinović
MentorDavor Juretić (mentor)
Committee memberDavor Juretić (predsjednik povjerenstva)
Committee memberJasna Puizina (član povjerenstva)
Committee memberLarisa Zoranić (član povjerenstva)
GranterUniversity of Split
Faculty of Science
(Department of Physics)
Split
Defense date and country2016-09-29, Croatia
Scientific / art field,
discipline and subdiscipline		NATURAL SCIENCES
Physics
Abstract
Hydrophobicity is one of the main attributes of amino acid side-chains. Hundreds of different hydrophobicity index scales, varying significantly in their contents and value ranges, were mainly created by, either experimental measurement, or theoretical calculations. In this thesis, a consensus hydrophobicity scale was developed. We have done a literature search using appropriate keywords and collected as many published hydrophobicity scales as we could find. These, together with more than 500 hydrophobicity scales from AAindex database, were all graded using an independently developed algorithm (Vukičević et al, to be published), which indicated a certain relationship with hydrophobicity. Also, the scales were inspected manually from the articles to examine the relation to hydrophobicity, thus ending up with a set of 159 scales used for developing the consensus. After the four different normalization types were performed, an averaging procedure was made for each, 4 crude consensus scales were obtained. Due to several scales having anomalous values for some amino acids, 4 filtering methods were used on each crude consensus scale. Identifying and processing the anomalous values resulted with 4 final consensus scales. Further analysis led to determining the best of these, the General Consensus Scale (GCS). Finally, the GCS and the values for proteinogenic amino acids, from the Molinspiration computational method, were correlated to the linear plot, allowing the extrapolation of Molinspiration values for various non-proteinogenic amino acids to the plot, and thus extending the GCS.
Abstract (croatian)
Hidrofobnost je jedna od glavnih karakteristika aminokiselinskih ostataka. Stotine različitih ljestvica hidrofobnosti, koje se znatno razlikuju po svom sadržaju i rasponu vrijednosti, su uglavnom nastale, ili eksperimentalnim mjerenjem, ili teoretskim proračunima. U ovom radu je izračunata konsenzusna ljestvica hidrofobnosti. Pretraživanjem literature pomoću odgovarajućih ključnih riječi, skupili smo sve ljestvice hidrofobnosti koje smo pronašli. Te su ljestvice, zajedno s 500 drugih iz AAindex baze podataka, ocijenjene korištenjem konstruiranog algoritma (Vukičević i suradnici, u pripremi), ukazujući na određenu povezanost s hidrofobnošću. Također, ljestvice su pojedinačno proučene iz odgovarajućih članaka, kako bi se ispitala veza s hidrofobnošću, što nas je dovelo do liste od 159 ljestvica iskorištenih za računanje konsenzusne ljestvice. Nakon što su provedene 4 vrste normalizacije, za svaku je izvršen postupak usrednjavanja i dobivene su 4 tzv. grube konsenzusne ljestvice. Neke od ljestvica sadržavale su naočigled nepravilne vrijednosti za određene aminokiseline, pa su napravljene po 4 metode filtriranja podataka za svaku grubu konsenzusnu ljestvicu. Pronalaženje i obrada takvih vrijednosti rezultirali su sa 4 konačne konsenzusne ljestvice. Daljnja analiza dovela je do utvrđivanja najbolje od njih, opće konsenzusne ljestvice (GCS). Na kraju, GCS i vrijednosti za proteinogene aminokiseline, dobivene kompjuterskom metodom Molinspiration, su linearno korelirane, čime je omogućena ekstrapolacija Molinspiration vrijednosti za razne neproteinogene aminokiseline. Na taj način je proširena GCS.
Keywords
Languageenglish
URN:NBNurn:nbn:hr:166:365242
Study programmeTitle: Physics; specializations in: major in teaching, major in Astrophysics, major in Biophysics, major in Enviromental physics, major in Computational physics
Course: major in Biophysics
Study programme type: university
Study level: graduate
Academic / professional title: magistar/magistra fizike (magistar/magistra fizike)
Type of resourceText
File originBorn digital
Access conditionsAccess restricted to students and staff of home institution
Terms of useLicence In copyright icon
Public noteKljučne riječi unio urednik.
Created on2017-10-10 14:25:17