Smoothed or Scaled Molecular Dynamics (Scaled MD)

A MD-based approach designed to increase the conformational space sampled by smoothing the system’s potential energy.

Smoothed or Scaled Molecular Dynamics (Scaled MD) can be performed using the following software tools:

• Amber
• Amber Tools

For examples of previously performed studies in which Smoothed or Scaled Molecular Dynamics (Scaled MD) was the primary method used, see the following example cases:

• Predicting Residence Time and Drug Unbinding Pathway through Scaled Molecular Dynamics.
• Enhanced Sampling Simulations of Ligand Unbinding Kinetics Controlled by Protein Conformational Changes.
• Smoothed Potential MD Simulations for Dissociation Kinetics of Etoposide To Unravel Isoform Specificity in Targeting Human Topoisomerase II.
• Structure, Thermodynamics, and Kinetics of Plinabulin Binding to Two Tubulin Isotypes
• Binding Residence Time through Scaled Molecular Dynamics: A Prospective Application to hDAAO Inhibitors.
• Exploring the PXR ligand binding mechanism with advanced Molecular Dynamics methods.
• Molecular Dynamics Simulations and Kinetic Measurements to Estimate and Predict Protein-Ligand Residence Times.
• Kinetics of protein-ligand unbinding via smoothed potential molecular dynamics simulations.

The folowing tutorial describes the use of Smoothed or Scaled Molecular Dynamics (Scaled MD):

• Estimation of relative residence times of protein-ligand complexes using Scaled Molecular Dynamics (ScMD, BikiNetics)