Absolute binding free energy calculations with explicit solvent molecular simulations can
provide estimates of protein-ligand affinities, and thus reduce the time and costs needed to …

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 …

A dataset of protein‐drug complexes with experimental binding energy and crystal structure
were analyzed and the performance of different docking engines and scoring functions (as …

Background: Design of small molecules which are able to bind to the protein responsible for
a disease is the key step of the entire process of the new medicine discovery. Atomistic …

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

The scoring function is one of the most important components in structure-based drug
design. Despite considerable success, accurate and rapid prediction of protein–ligand …

Over the past year there have been some interesting and significant advances in computer-
based ligand—protein docking techniques and related rational drug-design tools, including …

Many molecular docking programs are available nowadays, and thus it is of great practical
value to evaluate and compare their performance. We have conducted an extensive …

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 …

An empirical protein-ligand binding affinity estimation method, SCORE, was incorporated
into a popular docking program, DOCK4. The combined program, ScoreDock, was used to …