Molecular Dynamics as a Tool for Virtual Ligand Screening.

摘要: Rational drug design is essential for new drugs to emerge, especially when the structure of a target protein or catalytic enzyme known experimentally. To that purpose, high-throughput virtual ligand screening campaigns aim at discovering computationally binding molecules fragments inhibit particular interaction biological activity. The process often relies on docking methods which allow predicting molecule into with correct conformation and best possible affinity. method itself not sufficient as it suffers from several crucial limitations (lack flexibility information, no solvation effects, poor scoring functions, unreliable molecular affinity estimation).At interface computer techniques discovery, dynamics (MD) allows introducing before after protocol, refining protein-drug complexes in presence water, ions even membrane-like environments, ranking more accurate energy calculations. In this chapter we describe up-to-date MD protocols are mandatory supporting tools (VS) process. Using combination one computer-aided nowadays. It has proved its efficiency through many examples, described below.