In today’s world molecular biology, biochemistry and other biological fields are becoming increasingly information driven. Mainly the need of processing massive quantities of sequence information generated by recent developments in genome sequencing and proteome analysis has propelled these life sciences into a new era in which computer science, information technologies, and biology merged into a single discipline as bioinformatics. Accordingly genetics in conjunction with bioinformatics have been changing the old view in clinical diagnostics. By comprehensive genetic testing, individuals who are more susceptible to disease can be identified before any disease even exists. This way early predictive measures can be taken. Moreover personalized drug design, to tailor a specialized treatment based on your genetic makeup, seems to be a standard way of disease treatment in the near future.
In our department we concentrate on computer-aided drug design. In computer aided drug design a receptor molecule of the disease-causing mechanism is modelled in the computer. Succeedingly a drug molecule is designed to interact with the receptor molecule in such a way to fix malfunctioning mechanism of the protein. The candidate drug molecule can be a novel chemical structure which has been not synthesized before as well as a match from a database of already known drug molecules. This way of in silico computations of drug-enzyme interactions significantly shortens the process of experimental drug design for the target receptor.
Dynamics of the receptors to which drug molecules bind to is another field of study in our department. Understanding the functioning mechanism of the receptor is the very first step towards developing a way to interfere with its working mechanism. These receptor molecules are dynamic structures and the structural fluctuations in their dynamics is related to how they function Thus we are aiming to understand how these dynamic structures are functioning depending on different environment factors.
We are also interested in enhanced simulation techniques to investigate the functional dynamics of ion channel membrane proteins. Malfunctioning of ion channels is directly related to various neuro and neuromuscular diseases, such as epilepsy, Alzheimer’s, Parkinson’s and Huntington’s. These proteins are very hard to simulate due to the lack of experimental structural information in addition to their size when lipid bilayer is included. Thus enhanced sampling and simulation techniques, as well as advanced homology modelling methods are necessary for a better understanding of their dynamics.
Beta2-andrenergic receptors, phosphodiesterase IV, GABA-A receptors, nicotinic acetylcholine receptors, triosephosphate isomerase are some of the protein systems that we are also interested in.
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