Proteins interact with numerous water molecules to perform their physiological functions in
biological organisms. Most water molecules act as solvent media; hence, their roles may be …

Predicting protein–ligand binding affinities and the associated thermodynamics of
biomolecular recognition is a primary objective of structure-based drug design. Alchemical …

Due to the increasing amount of publicly available protein structures searching, enriching
and investigating these data still poses a challenging task. The Proteins Plus web service …

Exploration of the complex modulatory role of water in ligand–target binding is a current
challenge of drug design. This review reports on recent advances of prediction of water …

Accurate and efficient prediction of protein-ligand interactions has been a long-lasting
dream of practitioners in drug discovery. The insufficient treatment of hydration is widely …

Computer-aided drug design methods such as docking, pharmacophore searching, 3D
database searching, and the creation of 3D-QSAR models need conformational ensembles …

Scoring and numerical optimization of protein–ligand poses is an integral part of docking
tools. Although many scoring functions exist, many of them are not continuously …

Water is a key actor of various processes of nature and, therefore, molecular engineering
has to take the structural and energetic consequences of hydration into account. While the …

Molecular docking is one of the most widely used computational tools in structure-based
drug design and is critically dependent on accuracy and robustness of the scoring function …

Diphenylalanine (FF) peptides exhibit a unique ability to self-assemble into nanotubes with
confined water molecules playing pivotal roles in their structure and function. This study …