Prediction of ion-binding sites in proteins

Abstract

Title: Prediction of ion-binding sites in proteins Author: Nikola S ̌kardova ́ Department: Department of Cell Biology Supervisor: Mgr. Marian Novotny ́, Ph.D., Department of Cell Biology Abstract: Protein function is often mediated by interactions with other molecules, including ions, which bind to specific regions on proteins known as binding sites. These sites exhibit characteristic physicochemical and structural properties that can be exploited for their computational prediction. While experimental techniques provide highly accurate information about protein structures and binding sites, they are often time-consuming and costly. To address these limitations, a variety of computational methods have been developed to predict ion-binding sites from protein sequences and structures. The aim of this bachelor's thesis is to provide an overview and comparison of available computational methods and methodological approaches for the prediction of ion-binding sites in proteins. Keywords: ion-binding site, binding site prediction, computational methods, method comparison, proteins 1

Titul: Predikce vazebny ́ch mı 'st iontu ̊ v proteinech Autor: Nikola S ̌kardova ́ Katedra: Katedra bune ̌c ̌ne ́ biologie Vedoucı ́ pra ́ce: Mgr. Marian Novotny ́, Ph.D., Katedra bune ̌c ̌ne ́ biologie Abstrakt: Funkce proteinu ̊ je c ̌asto zprostr ̌edkova ́na interakcemi s dals ̌ı ́mi molekulami, vc ̌etne ̌ iontu ̊, ktere ́ se va ́z ̌ou na specificke ́ oblasti proteinu ̊ zna ́me ́ jako vazebna ́ mı 'sta. Tato mı 'sta vykazujı ́ charakteristicke ́ fyzika ́lne ̌-chemicke ́ a strukturnı ́ vlastnosti, ktere ́ lze vyuz ̌ı ́t pro jejich predikci pomocı ́ vy ́poc ̌etnı ́ch metod. Ac ̌koliv experimenta ́lnı ́ metody poskytujı ́ vysoce pr ̌esne ́ informace o struktur ̌e proteinu ̊ a jejich vazebny ́ch mı 'stech, jsou c ̌asto c ̌asove ̌ na ́roc ̌ne ́ a financ ̌ne ̌ na ́kladne ́. S cı ́lem tyto limity pr ̌ekonat byla vyvinuta r ̌ada vy ́poc ̌etnı ́ch metod pro predikci iontovy ́ch vazebny ́ch mı 'st z proteinovy ́ch sekvencı ́ a struktur. Cı ́lem te ́to bakala ́r ̌ske ́ pra ́ce je poskytnout pr ̌ehled a srovna ́nı ́ dostupny ́ch vy ́poc ̌etnı ́ch metod a metodologicky ́ch pr ̌ı 'stupu ̊ pro predikci iontovy ́ch vazebny ́ch mı 'st v proteinech. Klı ́c ̌ova ́ slova: vazebne ́ mı 'sto iontu ̊, predikce vazebny ́ch mı 'st, vy ́poc ̌etnı ́ metody, srovna ́nı ́ metod, proteiny 1