Virtual compound screening using molecular docking is widely used in the discovery of new lead compounds for drug design. However, this method is not completely reliable and therefore unsatisfactory. In this study, we used massive molecular dynamics simulations of protein-ligand conformations obtained by molecular docking in order to improve the enrichment performance of molecular docking. Our ...

We introduce the notion of Hopf algebroids, in which neither the total algebras nor the base algebras are required to be commutative. We give a class of Hopf algebroids associated to module algebras of the Drinfeld doubles of Hopf algebras when the Rmatrices act properly. When this construction is applied to quantum groups, we get examples of quantum groupoids, which are semi-classical limits o...

We present recent developments in the theory of Nambu mechanics, which include new examples of Nambu-Poisson manifolds with linear Nambu brackets and new representations of Nambu-Heisenberg commutation relations. Mathematics Subject Classification (1991) 70H99, 58F07

This chapter reviews the differential geometry-based solvation and electrolyte transport for biomolecular solvation that have been developed over the past decade. A key component of these methods is the differential geometry of surfaces theory, as applied to the solvent-solute boundary. In these approaches, the solvent-solute boundary is determined by a variational principle that determines the...

In this study conformation analysis of seven drugs commonly used in the treatment COVID-19 was performed. The most stable conformers drug molecules were as initial data for docking analysis. Using Cavityplus program, probable active binding sites both apo and holo forms main protease enzyme (Mpro) spike glycoprotein SARSCoV-2 receptors determined. interaction mechanisms 7 FDA approved (arbidol,...

We present recent developments in the theory of Nambu mechanics, which include new examples of Nambu-Poisson manifolds with linear Nambu brackets and new representations of Nambu-Heisenberg commutation relations. Mathematics Subject Classification (1991) 70H99, 58F07

We consider a point process i + ξi, where i ∈ Z and the ξi’s are i.i.d. random variables with variance σ. This process, with a suitable rescaling of the distribution of ξi’s, converges to the Poisson process in total variation for large σ. We then study a simple queueing system with our process as arrival process, and we provide a complete analytical description of the system. Although the arri...

Ionic diffusion through and near small domains is of considerable importance in molecular biophysics in applications such as permeation through protein channels and diffusion near the charged active sites of macromolecules. The motion of the ions in these settings depends on the specific nanoscale geometry and charge distribution in and near the domain, so standard continuum type approaches hav...

In this paper we re-express the Schouten-Nijenhuis, the Frölicher-Nijenhuis and the Nijenhuis-Richardson brackets on a symplectic space using the extended Poisson brackets structure present in the path-integral formulation of classical mechanics.

The epidermal growth factor receptor (EGFR) is a major target for drugs in treating lung carcinoma. Mutations in the tyrosine kinase domain of EGFR commonly arise in human cancers, which can cause drug sensitivity or resistance by influencing the relative strengths of drug and ATP-binding. In this study, we investigate the binding affinities of two tyrosine kinase inhibitors--AEE788 and Gefitin...