The research work in Biomolecular Structure and Function Group is centered on two most prominent problems in biomolecular sciences in 21st century. In the first project we are studying functional organization of the human genome, more specifically activation and inhibition of DNA methylation in human cells. In the second project we are working on neurodegenerative diseases, more specifically on development of novel drug candidates and early diagnostic methods for Alzheimer’s disease. (See Projects for details.) Different combination of the wet laboratory experiments and the computational studies are used to analyze the pathogenic processes at the molecular level. We have the active collaboration with the different academic laboratories and the pharmaceutical industry.
Computation and wet laboratory¶
We are using classical MD, QM, and QM/MM molecular modelling and simulation software, some of which are GROMACS, AutoDock Vina, RxDock, CP2K, GAMESS (US), VMD, PyMOL, UCSF Chimera, Avogadro, ChemAxon Marvin Suite, AmberTools via acpype, and Open Babel. Supplementary numerical analysis and graph plotting software packages such as LibreOffice Calc, R and Bio3D, SciDAVis, and gnuplot are used for analysis and visualization of simulation output. Combining the open source and proprietary computational chemistry software available software, we developed a mostly open source drug design pipelines to empower our research and increase efficiency of wet lab experiments. More info is available on the dedicated Software page.
For computations, we rely on the equipment of Computer Networks, Parallelization, and Simulation Laboratory (provided in part by NVIDIA under the GPU Education Center program) and Center for Advanced Computing and Modelling at the University of Rijeka. For wet lab experiments, we use equipment available at the Department of Biomedical Technology at the University of Rijeka.
We are developing novel drugs for Alzheimer’s disease in collaboration with Jiva Pharmaceuticals, a private pharmaceutical company.