Unit:
Κατεύθυνση ΒιοπληροφορικήΠληροφορική
Author:
Dalamara Katerina
Supervisors info:
Ευαγγελία Χρυσίνα, Κύρια Ερευνήτρια, ΕΙΕ, Αναπληρώτρια Καθηγήτρια, Örebro University, Sweden
Original Title:
Current state-of-the-art of the research conducted in mapping protein cavities – binding sites of bioactive compounds, peptides or other proteins
Translated title:
Current state-of-the-art of the research conducted in mapping protein cavities – binding sites of bioactive compounds, peptides or other proteins
Summary:
The aim of this thesis was to report on the current state-of-the-art of the research conducted concerning mapping of protein cavities with a potential function role as binding sites of bioactive compounds, peptides or other proteins.
A literature review was performed with emphasis on the relevant tools developed during the last decade. In addition, the main research findings regarding drug design and druggable targets based on binding sites are presented.
Processes performed in protein cavity detection and analysis, of previous research articles, are compared with the approach described by Anaxagoras Fotopoulos and Athanasios Papathanasiou (2015). The results showed that a competitive advantage of their approach is the multidimensional k-means algorithm for clustering.
For the bibliographic review the scientific knowledgebase has been used, which includes international articles and journals, book chapters, as well as online articles regarding drug design and protein cavity.
Search keywords such as protein cavity dynamics, catalytic sites of enzymes, protein pocket etc. were used to identify bioinformatics tools with text mining. A catalogue of the most recently developed tools is presented followed by a brief description of selected tools. The selection criteria imposed for preparing the catalogue and the detailed description included the publication date, as well as the algorithms and the methods they use. The tools were then classified according to the search keywords.
The findings of this research are discussed, and the algorithms and methods they use are compared, highlighting the advantages of protein cavity detection.
Main subject category:
Technology - Computer science
Keywords:
protein cavity dynamics, catalytic sites of enzymes, ligand binding, in silico docking, molecular dynamic simulations, active sites, protein pocket, protein conformer, rotamers
Number of references:
124
