Milestoning

Milestoning is an approach for estimating the characteristic time scales of slow processes by combining data from many short simulations.

Milestoning can be performed using the following software tools:

• BKiT
• SEEKR

For examples of previously performed studies in which Milestoning was the primary method used, see the following example cases:

• SEEKR2: Versatile Multiscale Milestoning Utilizing the OpenMM Molecular Dynamics Engine.
• Predicting Ligand Binding Kinetics Using a Markovian Milestoning with Voronoi Tessellations Multiscale Approach.
• Weighted ensemble milestoning (WEM): A combined approach for rare event simulations.
• Transient States and Barriers from Molecular Simulations and the Milestoning Theory: Kinetics in Ligand-Protein Recognition and Compound Design.
• ScMile: A Script to Investigate Kinetics with Short Time Molecular Dynamics Trajectories and the Milestoning Theory.
• Quantitative Ranking of Ligand Binding Kinetics with a Multiscale Milestoning Simulation Approach.
• SEEKR: Simulation Enabled Estimation of Kinetic Rates, A Computational Tool to Estimate Molecular Kinetics and Its Application to Trypsin-Benzamidine Binding.
• Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning.

Milestoning was also used in the following examples:

• Kinetics and free energy of ligand dissociation using weighted ensemble milestoning.