Path separation of dissipation-corrected targeted molecular dynamics simulations of protein-ligand unbinding
| Autor: | Wolf, Steffen, Post, Matthias, Stock, Gerhard |
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| Rok vydání: | 2022 |
| Předmět: | |
| Zdroj: | J. Chem. Phys. 158, 124106 (2023) |
| Druh dokumentu: | Working Paper |
| DOI: | 10.1063/5.0138761 |
| Popis: | 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. Comment: This preprint is the unedited version of a manuscript that has been published in J. Chen. Phys. and can be downloaded for private use only. Copyright with AIP and and the authors |
| Databáze: | arXiv |
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