# Path separation of dissipation-corrected targeted molecular dynamics simulations of protein-ligand unbinding

Source: [Path separation of dissipation-corrected targeted molecular dynamics simulations of protein-ligand unbinding](<https://www.sota2.com/research/paper/68fa43ce1e209131ce90ca18>)

Collection index: [llms.txt](<https://www.sota2.com/research/llms.txt>)

Data updated: 2025-10-25T04:29:46.571Z

Authors: Steffen Wolf, Matthias Post, Gerhard Stock

Published: 2022-12-14T10:54:03.000Z

## Abstract

Protein-ligand (un)binding simulations are a recent focus of biased molecular dynamics simulations. Such binding and unbinding can occur via different pathways in and out of a binding site. We here present a theoretical framework how to compute kinetics along separate paths and to combine the path-specific rates into global binding and unbinding rates for comparison with experiment. Using dissipation-corrected targeted molecular dynamics in combination with temperature-boosted Langevin equation simulations \[Nat. Commun. \\textbf{11}, 2918 (2020)\] applied to a two-dimensional model and the trypsin-benzamidine complex as test systems, we assess the robustness of the procedure and discuss aspects of its practical applicability to predict multisecond kinetics of complex biomolecular systems.

## Recorded benchmark results

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## Original sources and implementation

[Original paper](<https://arxiv.org/abs/2212.07154>)

[PDF](<https://arxiv.org/pdf/2212.07154.pdf>)