Introduction Nowadays, it is widely accepted that water molecules play a key role in binding
a ligand to a molecular target. Neglecting water molecules in the process of molecular …

The identification and optimization of lead compounds are inalienable components in drug
design and discovery pipelines. As a powerful computational approach for the identification …

Molecular dynamics (MD) and related methods are close to becoming routine computational
tools for drug discovery. Their main advantage is in explicitly treating structural flexibility and …

By using different evaluation strategies, we systemically evaluated the performance of
Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) and Molecular …

The use of methods at molecular scale for the discovery of new potential active ligands, as
well as previously unknown binding sites for target proteins, is now an established reality …

Binding free energy calculations that make use of alchemical pathways are becoming
increasingly feasible thanks to advances in hardware and algorithms. Although relative …

Accurate calculation of protein–protein binding free energy is of great importance in
biological and medical science, yet it remains a hugely challenging problem. In this work, we …

The pandemic caused by SARS-CoV-2 is currently representing a major health and
economic threat to humanity. So far, no specific treatment to this viral infection has been …

Key to the fragment optimisation process within drug design is the need to accurately
capture the changes in affinity that are associated with a given set of chemical modifications …

The infection by the 2019-nCoV coronavirus (COVID-19) is a world-wide emergency. The
crystal structure of a protein essential for virus replication has been filed in the Protein Data …