Introduction

This package is for running MD simulations useful for drug discovery.

New Protocol of the MD Stage in Lead Optimization

In the classic structure-based lead optimization (left in Figure New Protocol of the MD Stage in Lead Optimization), we’ve proposed the two MD stages at the bottom of the funnel: the light and fast MD screening stage, and the computationally more intense free energy calculation stage.

The Floes in the package for each MD stage are:

1. Light, fast MD screening

   1. Short Trajectory MD with Analysis Floe with 2 ns of the bound state production time

2. Relative binding free energy (RBFE)

   1. Ligand Bound and Unbound Equilibration for NES Floe

   2. Edge Mapper for RBFE calculations Floe

   3. Non-Equilibrium Switching Floe

You can use Equilibration and Non Equilibrium Switching Floe, which is the combined Floe of Ligand Bound and Unbound Equilibration for NES and Non-Equilibrium Switching Floes.

Or, you can simply combine the two MD stages and run

1. Short Trajectory MD with Analysis Floe with 6 ns of the bound state production time

2. Edge Mapper for RBFE calculations Floe

3. Non-Equilibrium Switching Floe

To get the information on the other Floes in the package, please refer to MDOrion Floes - Documentation in the left panel.