Scoring functions are a class of computational methods widely applied in structure-based
drug design for evaluating protein–ligand interactions. Dozens of scoring functions have …

Binding estimation after refinement (BEAR) is a novel automated computational procedure
suitable for correcting and overcoming limitations of docking procedures such as poor …

There is currently great interest in comparing protein–ligand docking programs. A review of
recent comparisons shows that it is difficult to draw conclusions of general applicability …

We have developed a new docking method, Pose‐Sensitive Inclined (PSI)‐DOCK, for
flexible ligand docking. An improved SCORE function has been developed and used in PSI …

The recognition process between a protein and a partner represents a significant theoretical
challenge. In silico structure-based drug design carried out with nothing more than the three …

The Protein Ligand Database (PLD) is a publicly available web-based database that aims to
provide further understanding of protein–ligand interactions. The PLD contains biomolecular …

Docking methodology aims to predict the experimental binding modes and affinities of small
molecules within the binding site of particular receptor targets and is currently used as a …

The prediction of the binding free energy between a ligand and a protein is an important
component in the virtual screening and lead optimization of ligands for drug discovery. To …

Given the three‐dimensional structure of a protein, how can one find the sites where other
molecules might bind to it? Do these sites have the properties necessary for high affinity …

Highlights•Reviewed scoring schemes and conformational sampling for protein–protein
complex structure prediction.•Discussed the database for binding affinity of complexes and …