Modeliranje 3D struktur interakcij med proteini in RNA : magistrsko delo

Čopar, Andrej (author), Curk, Tomaž (mentor)

Interakcije med proteini in RNA imajo ključno vlogo pri velikem številu celičnih procesov. Eksperimentalna analiza 3D struktur molekul je počasna in zahtevna, zato obstaja velika potreba po računskih metodah, ki uspešno napovedujejo mesta ter strukturo molekul v interakciji. V magistrskem delu smo definirali vrsto značilk, ki opisujejo lokalne lastnosti interakcij protein-RNA, na podlagi podatkov o 3D strukturah molekul protein-RNA. Razvili smo metodo, ki združuje strojno učenje in optimizacijski postopek za napovedovanje mesta interakcij med proteinom in RNA. Napovedi strojnega učenja se uporabijo za določanje začetnega stanja optimizacije. Optimizacijski postopek nato uporabi ocenjevalne funkcije osnovane na porazdelitvi 3D strukturnih značilk in tako predlaga najverjetnejšo pozicijo molekule RNA. Predlagani napovedni model dosega natančnost, ki je primerljiva z uspešnostjo najboljših obstoječih metod.

• Language: Slovenian
• Keywords: bioinformatika, interakcije protein-RNA, strukturna analiza, napovedni model, kombinatorična optimizacija, umestitev molekul, računalništvo, računalništvo in informatika, magisteriji
• Work type: Master's thesis/paper
• Typology: 2.09 - Master's Thesis
• Organization: FRI - Faculty of Computer and Information Science
• Publisher: A. Čopar
• Year: 2014
• Number of pages: 83 str.
• PID: 20.500.12556/RUL-29433
• COBISS.SI-ID: 1536019139
• Publication date in RUL: 04.09.2014

ČOPAR, Andrej, 2014, Modeliranje 3D struktur interakcij med proteini in RNA : magistrsko delo [online]. Master’s thesis. A. Čopar. [Accessed 30 March 2025]. Retrieved from: https://repozitorij.uni-lj.si/IzpisGradiva.php?lang=eng&id=29433

Secondary language

• Language: English
• Title: Modeling 3D structures of protein-RNA interactions

Abstract

Protein-RNA interactions have an essential role in many cellular processes. Experimental analysis of 3D molecular structure is slow and difficult process. Consequently, computational methods, which successfully predict interaction sites and molecular conformations are needed. In this thesis we have defined a number of attributes to describe local properties of protein-RNA interactions using data on 3D structure of protein-RNA molecules. We have implemented a method that uses machine learning and optimization algorithm for prediction of protein-RNA interaction sites. Machine learning predictions are used to generate initial positions for optimization. Optimization algorithm uses scoring functions based on the distribution of 3D structural attributes to identify most likely positions of the RNA molecule interacting with a given protein. The accuracy of the proposed prediction model is comparable to results obtained with best existing methods.

• Keywords: bioinformatics, protein-RNA interactions, structural analysis, prediction model, combinatorial optimization, molecular docking, computer science, computer and information science, master's degree