Protein–protein docking algorithms aim to predict the structure of a complex given the atomic
structures of the proteins that assemble it. The docking procedure usually consists of two …

A Monte Carlo simulation program (MONTY) has been developed to dock proteins onto
DNA. Protein and DNA interact via square-well potentials for hydrogen bond and van der …

Nucleic acid–ligand interactions play an important role in numerous cellular processes such
as gene function expression and regulation. Therefore, nucleic acids such as RNAs have …

Most life science processes involve, at the atomic scale, recognition between two molecules.
The prediction of such interactions at the molecular level, by so-called docking software, is a …

The prediction of ligand binding sites is an essential part of the drug discovery process.
Knowing the location of binding sites greatly facilitates the search for hits, the lead …

Protein‐nucleic acid interactions are involved in various cellular processes. Therefore,
determining the structures of protein‐nucleic acid complexes can provide insights into the …

DNA–protein interactions are involved in many essential biological activities. Because there
is no simple mapping code between DNA base pairs and protein amino acids, the prediction …

Nucleic acid (NA)–ligand interactions are of paramount importance in a variety of biological
processes, including cellular reproduction and protein biosynthesis, and therefore, NAs …

Recent developments in algorithms to predict the docking of two proteins have considered
both the initial rigid-body global search and subsequent screening and refinement. The …

In this review, we retraced the '40-year evolution'of molecular docking algorithms. Over the
course of the years, their development allowed to progress from the so-called 'rigid …