PaCS-Toolkit enables the execution of PaCS-MD (Parallel Cascade Selection Molecular Dynamic Simulation), a non-bias-enhanced sampling method, across various environments. Additionally, it offers tools for result analysis and visualization.
While PaCS-MD offers a wide range of applications with existing evaluation types, our toolkit also allows for the integration of additional types as needed.
We believe our package will benefit your research.
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[1] PaCS-Toolkit: Ikizawa, S., Hori, T., Wijana, T.N.*, Kono, H., Bai, Z., Kimizono, T., Lu, W., Tran, D.P., & Kitao, A. PaCS-Toolkit: Optimized software utilities for parallel cascade selection molecular dynamics (PaCS-MD) simulations and subsequent analyses. J. Phys. Chem. B., 128, 15, 3631-3642 (2024). https://doi.org/10.1021/acs.jpcb.4c01271
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[2] Original PaCS-MD or targeted-PaCS-MD (t-PaCS-MD): Harada, R., & Kitao, A. Parallel cascade selection molecular dynamics (PaCS-MD) to generate conformational transition pathway. J. Chem. Phys. 139, 035103 (2013). https://doi.org/10.1063/1.4813023
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[3] Dissociation PaCS-MD (dPaCS-MD): Tran, D. P., Takemura, K., Kuwata, K., & Kitao, A. Protein–Ligand Dissociation Simulated by Parallel Cascade Selection Molecular Dynamics. J. Chem. Theory Comput. 14, 404–417 (2018). https://doi.org/10.1021/acs.jctc.7b00504
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[4] Dissociation PaCS-MD (dPaCS-MD): Tran, D. P., & Kitao, A. Dissociation Process of a MDM2/p53 Complex Investigated by Parallel Cascade Selection Molecular Dynamics and the Markov State Model. J. Phys. Chem. B, 123, 11, 2469–2478 (2019). https://doi.org/10.1021/acs.jpcb.8b10309
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[5] Dissociation PaCS-MD (dPaCS-MD): Hata, H., Phuoc Tran, D., Marzouk Sobeh, M., & Kitao, A. Binding free energy of protein/ligand complexes calculated using dissociation Parallel Cascade Selection Molecular Dynamics and Markov state model. Biophysics and Physicobiology, 18, 305–31 (2021). https://doi.org/10.2142/biophysico.bppb-v18.037
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[6] Application to protein domain motion: Inoue, Y., Ogawa, Y., Kinoshita, M., Terahara, N., Shimada, M., Kodera, N., Ando, T., Namba, K., Kitao, A., Imada, K., & Minamino, T. Structural Insights into the Substrate Specificity Switch Mechanism of the Type III Protein Export Apparatus. Structure, 27 , 965-976 (2019). https://doi.org/10.1016/j.str.2019.03.017
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[7] Association and dissociation PaCS-MD (a/dPaCS-MD): Tran, D. P., & Kitao, A. Kinetic Selection and Relaxation of the Intrinsically Disordered Region of a Protein upon Binding. J. Chem. Theory Comput., 16, 2835–2845 (2020). https://doi.org/10.1021/acs.jctc.9b01203
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[8] Edge expansion PaCS-MD (eePaCS-MD): Takaba, K., Tran, D. P., & Kitao, A. Edge expansion parallel cascade selection molecular dynamics simulation for investigating large-amplitude collective motions of proteins. J. Chem. Phys. 152, 225101 (2020). https://doi.org/10.1063/5.0004654
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[9] Edge expansion PaCS-MD (eePaCS-MD): Takaba, K., Tran, D. P., & Kitao, A. Erratum: “Edge expansion parallel cascade selection molecular dynamics simulation for investigating large-amplitude collective motions of proteins” [J. Chem. Phys. 152, 225101 (2020)]. J. Chem. Phys. 153, 179902 (2020). https://doi.org/10.1063/5.0032465
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[10] rmsdPaCS-MD: Tran, D. P., Taira, Y., Ogawa, T., Misu, R., Miyazawa, Y., & Kitao, A. Inhibition of the hexamerization of SARS-CoV-2 endoribonuclease and modeling of RNA structures bound to the hexamer. Sci Rep 12, 3860 (2022). https://doi.org/10.1038/s41598-022-07792-2
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