Molecular Docking is used to positioning the computer-generated 3D structure of small
ligands into a receptor structure in a variety of orientations, conformations and positions …

Background: Design of small molecules which are able to bind to the protein responsible for
a disease is the key step of the entire process of the new medicine discovery. Atomistic …

Results of the combined use of the classical force field and the recent quantum chemical
PM7 method for docking are presented. Initially the gridless docking of a flexible low …

Discovery of new inhibitors of the protein associated with a given disease is the initial and
most important stage of the whole process of the rational development of new …

Preparation of the target-protein, particularly the protein protonation method can affect
considerably the spatial arrangement of the attached hydrogen atoms and the charge state …

The initial step of the rational drug design pipeline extremely needs an increase in
effectiveness. This can be done using molecular modeling: docking and molecular …

We present the novel docking algorithm based on the Tensor Train decomposition and the
TT-Cross global optimization. The algorithm is applied to the docking problem with flexible …

It is shown that the global energy minimum of a protein-ligand complex, when the energy is
calculated by the PM7 quantum-chemical semiempirical method with the COSMO implicit …

In this study several commonly used implicit solvent models are compared with respect to
their accuracy of estimating solvation energies of small molecules and proteins, as well as …

The following reasons limiting the accuracy of calculations of the protein—ligand binding
energy by the molecular docking programs are considered: the limited facilities of algorithms …