Automated molecular docking aims at predicting the possible interactions between two
molecules. This method has proven useful in medicinal chemistry and drug discovery …

Nwat-MMGBSA is a variant of MM-PB/GBSA based on the inclusion of a number of explicit
water molecules that are the closest to the ligand in each frame of a molecular dynamics …

Computational methods to calculate ligand binding affinities are increasing in popularity,
due to improvements in simulation algorithms, computational resources, and easy-to-use …

Water molecules are of great importance for the correct representation of ligand binding
interactions. Throughout the last years, water molecules and their integration into drug …

Water plays a major role in ligand binding and is attracting increasing attention in structure-
based drug design. Water molecules can make large contributions to binding affinity by …

Unquestionably, water appears to be an active player in the noncovalent protein–ligand
binding process, as it can either bridge interactions between protein and ligand or can be …

Neuropilin‐1 (NRP 1) is a transmembrane co‐receptor involved in binding interactions with
variety of ligands and receptors, including receptor tyrosine kinases. Expression of NRP 1 in …

Enhancing the binding affinities of ligands by means of lead modifications that displace
bridging water molecules at protein–ligand interfaces is an important and widely studied …

GPCR modeling approaches are widely used in the hit-to-lead (H2L) and lead optimization
(LO) stages of drug discovery. The aims of these modeling approaches are to predict the 3D …

To aid the evaluation of protein-protein complex model structures generated by protein
docking prediction (decoys), we previously developed a method to calculate the binding free …