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RAMD and its applications (using the implementation in NAMD) are described in: Kokh DB et. al. Estimation of Drug-Target Residence Times by τ-Random Acceleration Molecular Dynamics Simulations. J. Chem. Theory Comput.2018; DOI: 10.1021/acs.jctc.8b00230 Niu, Y., Li, S., Pan, D., Liu, H., Yao, X. Computational Study on the Unbinding Pathways of B-RAF Inhibitors and Its Implication for the Difference of Residence Time: Insight from Random Acceleration and Steered Molecular Dynamics Simulations. Phys. Chem. Chem. Phys. 2016, 18 (7),5622– 5629, DOI: 10.1039/C5CP06257H Xiaofeng Yu, Prajwal Nandekar, Ghulam Mustafa, Vlad Cojocaru, Galina I. Lepesheva and Rebecca C. Wade. Ligand tunnels in T. brucei and human CYP51: Insights for parasite-specific drug design. Biochim. Biophys. Acta (BBA) – General Subjects , (2016) 1860:67-78, DOI: 10.1016/j.bbagen.2015.10.015 Vlad Cojocaru, Peter J. Winn and Rebecca C. Wade, Multiple, Ligand-dependent Routes from the Active Site of Cytochrome P450 2C9. Curr. Drug. Metab. (2012) 13:143-154, DOI: 10.2174/138920012798918462 Vashisth, H., Abrams, C.F. Ligand escape pathways and (un)binding free energy calculations for the hexameric insulin-phenol complex. Biophys. J. 95, 4193-4204 (2008).DOI:10.1529/biophysj.108.139675 RAMD and its applications (using the implementation in AMBER unless otherwise specified) are described in: Lüdemann SK, Carugo O, Wade RC. Substrate access to cytochrome P450cam: a comparison of a thermal motion pathway analysis with molecular dynamics simulation data. J. Mol. Model. (1997) 3, 369-374. DOI:10.1007/s008940050053 (Initial ARGOS implementation) Luedemann, S.K., Lounnas, V. and R. C. Wade. How do Substrates Enter and Products Exit the Buried Active Site of Cytochrome P450cam ? 1. Random Expulsion Molecular Dynamics Investigation of Ligand Access Channels and Mechanisms. J Mol Biol, 303:797-811 (2000). doi:10.1002/jmbi.2000.4154 (First description of method and implementation in ARGOS) Luedemann, S.K., Gabdoulline,R.R., Lounnas, V. and R. C. Wade. Substrate access to cytochrome P450cam investigated by molecular dynamics simulations: An interactive look at the underlying mechanisms. Internet Journal of Chemistry, 4, 6 (2001). http://www.ijc.com/articles/2001v4/6/ (using the ARGOS implementation) Winn,P., Luedemann, S.K., Gauges,R., Lounnas, V. and R. C. Wade. Comparison of the dynamics of substrate access channels in three cytochrome P450s reveals different opening mechanisms and a new functional role for a buried arginine PNAS, 99, 5361-5366 (2002). Full text (using the ARGOS implementation) Schleinkofer, K., Sudarko, Winn,P., Luedemann, S.K. and R. C. Wade. Do mammalian cytochrome P450s show multiple ligand access pathways and ligand channelling? EMBO Reports, 6, 584-589 (2005).doi:10.1038/sj.embor.7400420 Carlsson, P., Burendahl, S., Nilsson, L. Unbinding of retinoic acid from the retinoic acid receptor by random expulsion molecular dynamics. Biophys. J. 91, 3151-3161 (2006).doi:10.1529/biophysj.106.082917 (Implementation in CHARMM) Wang, T., Duan, Y. Chromophore channeling in the G-protein coupled receptor rhodopsin. J. Am. Chem. Soc. 129, 6970-6971 (2007).doi:10.1021/ja0691977 Long, D., Mu, Y. Yang, D. Molecular Dynamics Simulation of Ligand Dissociation from Liver Fatty Acid Binding Protein. PLoS ONE 4, e6801 (2008).doi:10.1371/journal.pone.0006081 (Implementation of a variant of RAMD in GROMACS) Perakyla, M. Ligand unbinding pathways from the vitamin D receptor studied by molecular dynamics simulations. 38, 185-198 (2009).doi:10.1007/s00249-008-0369-x Klvana, M. et al. Pathways and Mechanisms for Product Release in the Engineered Haloalkane Dehalogenases Explored Using Classical and Random Acceleration Molecular Dynamics Simulations J. Mol. Biol. 392, 1339-1356 (2009).doi:10.1016/j.jmb.2009.06.076 Pavlova, M. et al. Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate Nature Chem. Biol. 5, 727-733 (2009).doi:10.1038/nchembio.205 Wang, T., Duan, Y. Ligand entry and exit pathways in the beta2-adrenergic receptor. J. Mol. Biol. 392, 1102-1115 (2009).doi:10.1016/j.jmb.2009.07.093 Tutorial on application of RAMD A tutorial describing the τRAMD process of setting up and running RAMD simulations for estimation of the relative residence time (τ) of a protein-small molecule complex can be found here.