SARS-CoV-2 PLpro was investigated as a therapeutic target for potent antiviral drugs due to its essential role in not only viral replication but also regulating the inborn immune response. Several computational approaches, including homology modelling, molecular docking, and dynamics (MD) studies, were employed search promising treating SARS-CoV-2. Eighty-one compounds, sub-structurally similar...

DYRK kinases are involved in alternative pre-mRNA splicing as well as in neuropathological states such as Alzheimer’s disease and Down syndrome. In this study, we present the design, synthesis, and biological evaluation of indirubins as DYRK inhibitors with enhanced selectivity. Modifications of the bis-indole included polar or acidic functionalities at positions 5′ and 6′ and a bromine or a tr...

The field of molecular modeling has long recognized modeling the folding, assembly, and long-time dynamics of large macromolecules as its biggest challenge, since it is precisely at large size and long time scales that computational methods are most taxed. In response, many methods have been developed to reduce the computational cost by coarsening the granularity of the problem. Inevitably accu...

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In the recent years, lattice modelling proved to be a topic of renewed interest. Indeed, fields as distant as chemical modelling and biological tissue modelling use network models that appeal to similar equilibrium laws. In both cases, obtaining an equivalent continuous model allows to simplify numerical procedures. We describe an homogenization technique designed for discrete structures that p...

Molecular modeling and simulation has been recognized as an effective tool for gaining a comprehensive and insightful understanding of nanomaterial structure-property relationships, which are critical for nanomaterial development. Note that nanomaterial development is a very complicated task involving the design and management of massive runs of simulations and numerous types of subtasks in mul...

Computer graphics experiments led to examples where the graphical approximant is ambient isotopic to a spline, but a slight perturbation of the approximant destroys the isotopic equivalence. These serve as cautionary counterexamples for dynamic visualization of molecular simulations. These visual experiments facilitated the creation of a new operation on splines and formal proofs of its converg...

In the development of drugs intended for oral use, good drug absorption and appropriate drug delivery are very important. Now the predictions for drug absorption and oral bioavailability follow similar approach: calculate molecular descriptors for molecules and build the prediction models. This approach works well for the prediction of compounds which cross a cell membrane from a region of high...