posted on 2021-12-08, 12:34authored byCong Liu, Emiliano Brini, Ken A. Dill
Molecular docking
algorithms are used to seek the most active compounds
from a pool of ligands. In principle, molecular dynamics (MD) simulations
with accurate physical potentials and sampling could yield better
enrichments, but they are computationally expensive. Here, we describe a method called MELD-Bracket that utilizes biased replica exchange ladders in MD in order to
compete different ligands against each other within a fast bracket
style “binding tournament”. MELD-Bracket finds best-binders
rapidly when ligands are well separated in their binding affinities.