Ensemble docking corresponds to the generation of an" ensemble" of drug target
conformations in computational structure-based drug discovery, often obtained by using …

Abstract 3D pharmacophore models are three‐dimensional ensembles of chemically
defined interactions of a ligand in its bioactive conformation. They represent an elegant way …

Molecular docking has become an increasingly important tool for drug discovery. In this
review, we present a brief introduction of the available molecular docking methods, and their …

Molecular docking is a widely-used computational tool for the study of molecular recognition,
which aims to predict the binding mode and binding affinity of a complex formed by two or …

The field of structure-based drug design is a rapidly growing area in which many successes
have occurred in recent years. The explosion of genomic, proteomic, and structural …

The term molecular mechanics (MM) refers to the use of simple potential-energy functions
(eg, harmonic oscillator or Coulombic potentials) to model molecular systems. Molecular …

The docking field has come of age. The time is ripe to present the principles of docking,
reviewing the current state of the field. Two reasons are largely responsible for the maturity …

Pharmacology over the past 100 years has had a rich tradition of scientists with the ability to
form qualitative or semi‐quantitative relations between molecular structure and activity in …

A rational approach is needed to maximize the chances of finding new drugs, and to exploit
the opportunities of potential new drug targets emerging from genomic and proteomic …

An increasing number of studies have reported computations of the standard (absolute)
binding free energy of small ligands to proteins using molecular dynamics (MD) simulations …