PhD Topics

1. Characterizing sequence-structure-function relationships: A multi-dimensional approach for evaluating similarity in structural biology data

Supervisor: prof. Jaroslav Koča

Consultants: Crina-Maria Ionescu, Ph.D.

Annotation: Understanding the similarity between the sequence and/or structure of biomolecules has been key to inferring evolutionary relationships and predicting the function of biomolecules. We propose a novel approach for defining and evaluating the similarity between biomolecules. The approach is based on representing structural biology data as a square matrix of biomolecular structure elements and their properties; we then define similarity as the result of comparing the eigenvalues and eigenvector spaces determined for the biomolecules compared. Such a test of statistical similarity is intended to determine whether the compared biomolecules share features of structure, function, biological pathway, or affinity for a certain range of binding partners.

RG: Jaroslav Koča Research Group

Keywords: biomolecules, sequence-structure-function relationship, data analysis

2. Structural biology of ion channels

Supervisor: prof. Jaroslav Koča

Consultant: Crina-Maria Ionescu, Ph.D.

Annotation: Ion channels, which are ubiquitous throughout all domains of life, facilitate communication across the cell membrane and are thus responsible for a wide array of physiological processes. However, structural studies of ion channels are challenging because of the large size, complex structure, and membrane localization of these proteins. The project has two dimensions. One dimension refers to creating knowledge resources that compiles literature evidence regarding the properties and function of various parts of the molecule (e.g., agonist binding sites, channel gating area, regulatory sites, etc.), and provides such knowledge in an easily accessible manner (e.g., web server). This will facilitate structural and functional studies on ion channels. The second aspect refers to expanding the understanding of the functioning and dysfunction of ion channels. To this end, the PhD candidate will use well-established tools, including those developed in our lab (e.g., MOLE, ACC, CrocoBLAST, CrocoPhylogeny).

RG: Jaroslav Koča Research Group

Keywords: biomolecule, membrane protein, bioinformatics