On 24th January, our colleague Ivana Hutařová Vařeková successfully defended her dissertation thesis at the Faculty of Informatics, Masaryk University. The topic of her thesis is "The visualization of secondary structure elements of proteins in 2D".
The thesis focuses on protein domains and their grouping into protein families with similar structures and biological functions. The state of the art was that no software could visualise secondary structure elements within protein families and take into account the 3D structure of a domain. Ivana set out to remedy this deficiency. First, she co-developed a unified nomenclature of equivalent structure elements found in different domains. Results of this work are available in the software tools SecStrAnnotator and OverProt. Then, Ivana developed an algorithm for automatically generating 2D diagrams of single domains and whole families that consider the 3D structure of every domain involved and can produce. Pre-computed results for the entire PDB are available in our 2DProts database, while the innovative diagram-generating software is integrated into the widely established CATH database.
Congratulations, Ivana!
PDBCharges, a tool providing partial atomic charges for protein structures from the Protein Data Bank, was published in the journal Nucleic Acids Research.
