Original title: Benchmarking výpočetních nástrojů pro predikci vlivu mutací na stabilitu proteinů
Translated title: Benchmark of the Computational Tools for the Prediction of the Effect of Mutations on Protein Stability
Authors: Berezný, Matej ; Martínek, Tomáš (referee) ; Musil, Miloš (advisor)
Document type: Master’s theses
Year: 2024
Language: eng
Publisher: Vysoké učení technické v Brně. Fakulta informačních technologií
Abstract: [eng] [cze]
Návrh proteínov vyžaduje informáciu o tom ako mutácie ovplyvňujú celkovú stabilitu proteinu. Pre tento prípad existuje mnoho verejne dostupných nástrojov avšak ich kolektívne používanie či porovnávanie je veľmi pracné. Presne pre tento prípad som vyvinul BenchStab; konzolovú aplikáciu/Python knižnicu navrhnutú pre rýchlu a priamočiaru manipuláciu s 18 prediktormi, umožňujúc hromadné získavanie mutačných výsledkov. Zároveň som vytvoril novú unikátnu dátovú sadu, získanú z FireProtDB. Tento dataset som použil na porovnanie 24 rôznych predikčných metód pomocou rôznych metrík. Protein design necessitates understanding how mutations influence their stability. Numerous online predictors exist for this aim, but it is challenging to compare them or to use them collectively. For that purpose I developed BenchStab, a console application/Python package designed for the swift and straightforward operation of 18 predictors, gathering results from a series of mutants. Benchstab is freely available on GitHub and can be expanded to include more predictors. To avoid potential dataset bias towards some predictors, I have constructed a new unique dataset, sourced from FireProtDB. I utilized this dataset to assess 24 distinct prediction methods from the three different perspectives.
Keywords: benchmark; benchmark stability proteínov; dataset; DDG; DDMut; FoldX4; Foldx5; Maestro; mutácie; PoPMuSiC; predikcia; prediktor; proteín; sekvencia; softvérový nástroj; stabilita; stabilita proteínov; webový klient; získavanie stability; štruktúra; benchmark; dataset; DDG; DDMut; FoldX4; Foldx5; Maestro; mutations; PoPMuSiC; prediction; predictor; protein; protein stability; protein stability benchmark; protein stability predictor; sequence; software tool; stability; stability querying; structure; web-tool client

Institution: Brno University of Technology (web)
Document availability information: Fulltext is available in the Brno University of Technology Digital Library.
Original record: https://hdl.handle.net/11012/248562

Permalink: http://www.nusl.cz/ntk/nusl-618986


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Universities and colleges > Public universities > Brno University of Technology
Academic theses (ETDs) > Master’s theses