Publicaties
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Modeling the reactivity and selectivity of chemical reactions with advanced molecular modeling methods Universiteit Gent
Homology modeling, molecular docking, and dynamics of two alpha-methyl-D-mannoside-specific lectins from Arachis genus Universiteit Gent
The Arachis genus belongs to the Dalbergieae tribe, a group of plants that show promising potential novel lectins. Three lectins of the well-known Arachis hypogaea have already been purified, while lectins from related species are still unknown. Genomes of two closely related species, Arachis duranensis and Arachis ipaensis, were recently sequenced. Therefore, this study aimed to establish the three-dimensional structure of Arachis duranensis ...
Molecular dynamics and docking simulations as a proof of high flexibility in E. coli FabH and its relevance for accurate inhibitor modeling Vrije Universiteit Brussel
Bacterial beta-ketoacyl-acyl carrier protein synthase III (FabH) has become an attractive target for the development of new antibacterial agents which can overcome the increased resistance of these pathogens to antibiotics in clinical use. Despite several efforts have been dedicated to find inhibitors for this enzyme, it is not a straightforward task, mainly due its high flexibility which makes difficult the structure-based design of FabH ...
Structural investigation of human cystine/glutamate antiporter system xc− (Sxc−) using homology modeling and molecular dynamics Vrije Universiteit Brussel
The cystine/glutamate antiporter system xc− (Sxc−) belongs to the SLC7 family of plasma membrane transporters. It exports intracellular glutamate along the latter’s concentration gradient as a driving force for cellular uptake of cystine. Once imported, cystine is mainly used for the production of glutathione, a tripeptide thiol crucial in maintenance of redox homeostasis and protection of cells against oxidative stress. Overexpression of ...
Operando modeling of zeolite-catalyzed reactions using first-principles molecular dynamics simulations Universiteit Gent
Within this Perspective,we critically reflect on the role of first-principlesmolecular dynamics (MD) simulations in unraveling the catalytic functionwithin zeolites under operating conditions. First-principles MD simulationsrefer to methods where the dynamics of the nuclei is followed in timeby integrating the Newtonian equations of motion on a potential energysurface that is determined by solving the quantum-mechanical many-bodyproblem for the ...
Molecular modeling, docking and dynamics simulations of the Dioclea lasiophylla Mart. Ex Benth seed lectin : an edematogenic and hypemociceptive protein Universiteit Gent
Molecular Modeling of the Synthesis of Zeolites and Related Nanoporous Materials Universiteit Gent
Zeolites are microporous inorganic crystals with a framework that mainly contains silicon, oxygen and aluminum. The chemical composition is comparable to quartz, but the crystal structure is fundamentally different. Zeolites contain regular cavities (channels and cages) with a maximum diameter of 1.2 nanometer, large enough to contain small organic molecules. The walls of the cavities represent a huge internal surface (of the order of 1000 ...
In Silico Modeling of Osteochondral Pathophysiology and Regeneration. Identification of Molecular Signatures and Therapeutic Targets with Mechanistic and Data-Driven Network Models KU Leuven
"In silico modeling of osteochondral pathophysiology and regeneration:
Identification of molecular signatures and drug targets with mechanistic and data-driven network models" Chondrocyte maturation and cartilage to bone transition in the context of the growth plate development and osteoarthritis (OA) is a process that is thoroughly regulated with inputs from multiple biochemical and mechanical signals active at multiple length scales. We ...
Identification of molecular signatures and drug targets with mechanistic and data-driven network models" Chondrocyte maturation and cartilage to bone transition in the context of the growth plate development and osteoarthritis (OA) is a process that is thoroughly regulated with inputs from multiple biochemical and mechanical signals active at multiple length scales. We ...
Comparison of the complexation between methylprednisolone and different cyclodextrins in solution by 1H-NMR and molecular modeling studies KU Leuven
Complexation in solution between methylprednisolone and three different cyclodextrins [2-hydroxypropyl-b-cyclodextrin (HP-b-CD), g-cyclodextrin (g-CD), and 2-hydroxypropyl- g-cyclodextrin (HP-g-CD)] was studied using phase solubility analysis, one and twodimensional 1H-NMR and molecular modeling. Estimates of the complex formation constant (K1:1) show that the tendency of methylprednisolone to complex with CDs follows the order: ...