Rational drug design is essential for new drugs to emerge, especially when the structure of a target protein or nucleic acid is known. To that purpose, high-throughput virtual ligand screening campaigns aim at discovering computationally new binding molecules or fragments to modulate particular biomolecular interactions or biological activities, re...
BackgroundSialic acids are essential monosaccharides influencing several biological processes and disease states. The sialyltransferases catalyze the transfer of Sia residues to glycoconjugates playing critical roles in cellular recognition and signaling. Despite their importance, the molecular mechanisms underlying their substrate specificity, esp...
peer reviewed
A crucial aspect in the simulation of electrochemical interfaces consists in treating the distribution of electronic charge of electrode materials that are put in contact with an electrolyte solution. Recently, it has been shown how a machine-learning method that specifically targets the electronic charge density, also known as SALTED, can be used ...
As the protolunar disk formed by the giant impact with the incoming asteroid Theia started to cool, the Earth condensed in its center as a molten planet. The outer layer, rich in lithophile oxides, formed the magma ocean, whose dynamical behavior heavily influenced the entire evolution of the early Earth. Here, we employ first-principles molecular ...
Little research has been conducted to determine the thermal properties and phenomena of graphane and fluorographene. A clear understanding of the thermal problems involved is needed, which may provide a basis for further research on other material properties. In the present study, molecular dynamics simulations were performed to investigate the the...
In spite of significant efforts to investigate the ability of hydrogenated and fluorinated graphene to conduct heat, little research has focused particularly upon their other thermal properties, such as thermal contraction and heat capacity, which have implications for the development of thermal nanotechnology. In an attempt to determine these ther...
To develop therapeutic strategies against COVID-19, we introduce a high-resolution all-atom polarizable model capturing many-body effects of protein, glycans, solvent, and membrane components in SARS-CoV-2 spike protein open and closed states. Employing $\mu$s-long molecular dynamics simulations powered by high-performance cloud-computing and unsup...
Published in Molecular diversity
Manipulating intracellular signals by interaction with transmembranal G-protein-coupled receptors (GPCRs) is the way of action of more than 30% of available medicines. Designing molecules against GPCRs is most challenging due to their flexible binding orthosteric and allosteric pockets, a property that lead to different mode and extent of activatio...
Published in Molecular diversity
Cancer is one of the life-threatening diseases and the second leading cause of death in the world. The estrogen receptor can be considered as one of the significant drug targets for cancer. A large number of clinically used anticancer drugs were identified from phytochemicals. Multiple literatures suggested that extracts of Datura sp. significantly...
