Computer-aided drug design (CADD) is one of the pivotal approaches to contemporary pre-
clinical drug discovery, and various computational techniques and software programs are …

One of the largest challenges of computational chemistry is calculation of accurate free
energies for the binding of a small molecule to a biological macromolecule, which has …

Docking is one of the most commonly used techniques in drug design. It is used for both
identifying correct poses of a ligand in the binding site of a protein as well as for the …

In this research, through the use of molecular dynamics (MD) simulations, the ability of gold
nanoparticles (AuNPs) functionalized by different groups, such as 3-mercaptoethylsulfonate …

The enzyme subclass of glycosyltransferases (GTs; EC 2.4) currently comprises 97 families
as specified by CAZy classification. One of their important roles is in the biosynthesis of …

Analysis of the literature involving computational modeling of diseases and drug design with
the aid of experimental spectroscopic techniques reveals that this specific combination of …

The binding free energies (Δ G Bind) obtained from molecular mechanics with Poisson–
Boltzmann surface area (MM-PBSA) or molecular mechanics with Generalized Born surface …

We studied the pH-dependence of ribosome catalyzed peptidyl transfer from fMet-tRNAfMet
to the aa-tRNAs Phe-tRNAPhe, Ala-tRNAAla, Gly-tRNAGly, Pro-tRNAPro, Asn-tRNAAsn …

Accurate ligand-protein binding affinity prediction, for a set of similar binders, is a major
challenge in the lead optimization stage in drug development. In general, docking and …

A broad range of computational methods exist for the estimation of ligand–protein binding
affinities. In this chapter we will provide a guide to the linear interaction energy (LIE) method …