PhD. Topics
Institute of Chemistry
Topic
Analysis of Protein Structure and Dynamics through the Lens of Algorithmic Approachesmics
PhD. program
Physical chemistry
Name of the supervisor
Ing. Vladimír Sládek, PhD.
Contact:
Receiving school
Faculty of Natural Sciences, Commenius University Bratislava
Annotation
Currently available methods for the analysis of protein structure and dynamics integrate several scientific
disciplines. The students contribution is aimed towards combining aspects of first-principles calculations (ab
initio), classical (atomistic) molecular dynamics (MD) and network theory. Accent will be put on the
development and testing of network model(s) based on data from first-principles and MD simulations will be
accented in this work. Practical applications include identification of relevant amino acid residues in
processes such as ligand binding to enzymes, protein-protein interactions in cellular signalling cascades etc.
The goal is to yield qualitative and quantitative predictions in the field of proteomics (or molecular biology).
disciplines. The students contribution is aimed towards combining aspects of first-principles calculations (ab
initio), classical (atomistic) molecular dynamics (MD) and network theory. Accent will be put on the
development and testing of network model(s) based on data from first-principles and MD simulations will be
accented in this work. Practical applications include identification of relevant amino acid residues in
processes such as ligand binding to enzymes, protein-protein interactions in cellular signalling cascades etc.
The goal is to yield qualitative and quantitative predictions in the field of proteomics (or molecular biology).