Institute of Chemistry
Topic
Multiscale methods for the analysis of protein structure and dynamics
PhD. program
Physical chemistry
Name of the supervisor
Ing. Vladimír Sládek, PhD.
Contact:
Receiving school
Faculty of Chemical and Food Technology, Slovak University of Technology
Annotation
The thesis is aimed at further development of theoretical methods for the analysis of protein
structure and dynamics which are presently available. The multi-scale aspect of the approach is
determined by combining aspects of first-principles calculations (ab initio), classical (atomistic)
molecular dynamics (MD) and network theory. The goal is to yield qualitative and quantitative
predictions in the field of proteomics (or molecular biology). These methods fall under the umbrella
of computational, in silico, approaches. 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 key amino acid residues in processes such as ligand binding to enzymes,
protein-protein interactions in cellular signalling cascades etc. The tuning and validation of the
methodology will be on real-world bio-systems in collaboration with organo-synthetic and biology
groups.
structure and dynamics which are presently available. The multi-scale aspect of the approach is
determined by combining aspects of first-principles calculations (ab initio), classical (atomistic)
molecular dynamics (MD) and network theory. The goal is to yield qualitative and quantitative
predictions in the field of proteomics (or molecular biology). These methods fall under the umbrella
of computational, in silico, approaches. 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 key amino acid residues in processes such as ligand binding to enzymes,
protein-protein interactions in cellular signalling cascades etc. The tuning and validation of the
methodology will be on real-world bio-systems in collaboration with organo-synthetic and biology
groups.