Modern simulation and modeling approaches to investigation of biomolecular structure and
function rely heavily on a variety of methods—water models—to approximate the influence …

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 …

Equilibrium simulations of molecular systems allow to extract many physicochemical
properties. Given an “accurate enough” model, a “large enough” simulation system and …

The ability to design customized proteins to perform specific tasks is of great interest. We are
particularly interested in the design of sensitive and specific small molecule ligand‐binding …

This paper focuses on the computationally assisted design of molecularly imprinted
polymers (MIP), emphasizing the selected strategies and chosen methods of approach. In …

The need for accurate yet efficient representation of the aqueous environment in
biomolecular modeling has led to the development of a variety of generalized Born (GB) …

Accuracy of protein–ligand binding free energy calculations utilizing implicit solvent models
is critically affected by parameters of the underlying dielectric boundary, specifically, the …

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 …

Computational methods, including density functional theory, are proving to be powerful
approaches to tame the otherwise overwhelming selection of optimal species and …

PDZ domains generally bind short amino acid sequences at the C-terminus of target
proteins, and short peptides can be used as inhibitors or model ligands. Here, we used …