Middle-way flexible docking: Pose prediction using mixed-resolution Monte Carlo in estrogen receptor α.

ABSTRACT: There is a vast gulf between the two primary strategies for simulating protein-ligand interactions. Docking methods significantly limit or eliminate protein flexibility to gain great speed at the price of uncontrolled inaccuracy, whereas fully flexible atomistic molecular dynamics simulations are expensive and often suffer from limited sampling. We have developed a flexible docking approach geared especially for highly flexible or poorly resolved targets based on mixed-resolution Monte Carlo (MRMC), which is intended to offer a balance among speed, protein flexibility, and sampling power. The binding region of the protein is treated with a standard atomistic force field, while the remainder of the protein is modeled at the residue level with a Gō model that permits protein flexibility whil

SUBMITTER: Spiriti J 

PROVIDER: S-EPMC6478315 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature