Multidimensional reaction rate theory with anisotropic diffusion.

An analytical expression is derived for the rate constant that describes diffusive transitions between two deep wells of a multidimensional potential. The expression, in contrast to the Kramers-Langer formula for the rate constant, is valid even when the diffusion is highly anisotropic. Our approach is based on a variational principle for the reactive flux and uses a trial function for the splitting probability or commitor.

Both protein dynamics and ligand concentration can shift the binding mechanism between conformational selection and induced fit.

This study aimed to shed light on the long debate over whether conformational selection (CS) or induced fit (IF) is the governing mechanism for protein-ligand binding. The main difference between the two scenarios is whether the conformational transition of the protein from the unbound form to the bound form occurs before or after encountering the ligand. Here we introduce the IF fraction (i.

BDflex: a method for efficient treatment of molecular flexibility in calculating protein-ligand binding rate constants from brownian dynamics simulations.

A method developed by Northrup et al. [J. Chem.