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projects:tauramddescription [2019/06/07 09:15] richter created |
projects:tauramddescription [2020/09/28 16:47] (current) kokhadmin [RAMD and its applications (using the implementation in Gromacs) are described in:] |
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| - | RAMD and its applications (using the implementation in NAMD) are described in: | + | =====References===== |
| - | 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 | + | ====RAMD and its applications (using the implementation in Gromacs) are described in:==== |
| - | 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 | + | * Kokh DB et. al. A Workflow for Exploring Ligand Dissociation from a Macromolecule: Efficient Random Acceleration Molecular Dynamics Simulation and Interaction Fingerprints Analysis of Ligand Trajectories. J. Chem. Phys. 153, 125102 (2020); https://doi.org/10.1063/5.0019088 or **arXiv** 2020 [[https://arxiv.org/abs/2006.11066|arXiv:2006.11066]] |
| - | 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 | + | ====RAMD and its applications (using the implementation in NAMD) are described in:==== |
| - | 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 | + | * Kokh DB et. al. Machine Learning Analysis of τRAMD Trajectories to Decipher Molecular Determinants of Drug-Target Residence Times. Front. Mol. Biosci. 2019 [[https://www.frontiersin.org/articles/10.3389/fmolb.2019.00036/full|DOI: 10.1021/acs.jctc.8b00230]] |
| - | 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 | + | * Kokh DB et. al. Estimation of Drug-Target Residence Times by τ-Random Acceleration Molecular Dynamics Simulations. J. Chem. Theory Comput. 2018, **14**, 7, 3859–3869 2018 [[https://pubs.acs.org/doi/abs/10.1021/acs.jctc.8b00230|DOI: 10.1021/acs.jctc.8b00230]] |
| - | RAMD and its applications (using the implementation in AMBER unless otherwise specified) are described in: | + | * 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, [[http://pubs.rsc.org/en/content/articlelanding/2016/cp/c5cp06257h#!divAbstract|DOI: 10.1039/C5CP06257H]] |
| - | 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) | + | * 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, [[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4689311/|DOI: 10.1016/j.bbagen.2015.10.015]] |
| - | 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) | + | * 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, [[http://www.eurekaselect.com/75602/article|DOI: 10.2174/138920012798918462]] |
| - | 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) | + | * 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). [[http://dx.doi.org/10.1529/biophysj.108.139675|DOI:10.1529/biophysj.108.139675]] |
| - | 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 | + | ====RAMD and its applications (using the implementation in AMBER unless otherwise specified) are described in==== |
| - | 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) | + | * 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. [[https://link.springer.com/article/10.1007%2Fs008940050053|DOI:10.1007/s008940050053]] (Initial ARGOS implementation) |
| - | 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 | + | * 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). [[http://dx.doi.org/10.1006/jmbi.2000.4154|doi:10.1002/jmbi.2000.4154]] (First description of method and implementation in ARGOS) |
| - | 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) | + | * 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). [[ |
| - | 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 | + | http://www.ijc.com/articles/2001v4/6/|http://www.ijc.com/articles/2001v4/6/]] (using the ARGOS implementation) |
| - | 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 | + | * 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). [[http://www.pnas.org/cgi/content/full/99/8/5361|Full text]] (using the ARGOS implementation) |
| - | 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 | + | * 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). [[http://dx.doi.org/10.1038/sj.embor.7400420|doi:10.1038/sj.embor.7400420]] |
| - | 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 | + | * 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).[[http://dx.doi.org/10.1529/biophysj.106.082917|doi:10.1529/biophysj.106.082917]] (Implementation in CHARMM) |
| - | Tutorial on application of RAMD | + | * Wang, T., Duan, Y. Chromophore channeling in the G-protein coupled receptor rhodopsin J. Am. Chem. Soc. 129, 6970-6971 (2007).[[http://dx.doi.org/10.1021/ja0691977|doi:10.1021/ja0691977]] |
| - | 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. | + | * Long, D., Mu, Y. Yang, D. Molecular Dynamics Simulation of Ligand Dissociation from Liver Fatty Acid Binding Protein. PLoS ONE 4, e6801 (2008).[[http://dx.doi.org/10.1371/journal.pone.0006081|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).[[http://dx.doi.org/10.1007/s00249-008-0369-x|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). [[http://dx.doi.org/10.1016/j.jmb.2009.06.076|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). [[http://dx.doi.org/10.1038/nchembio.205|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). [[http://dx.doi.org/10.1016/j.jmb.2009.07.093|doi:10.1016/j.jmb.2009.07.093]] | ||
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| + | =====Tutorials on the application of RAMD===== | ||
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| + | === Implementation in NAMD === | ||
| + | A tutorial describing the τRAMD process of setting up and running [[https://www.h-its.org/downloads/ramd/|RAMD]] simulations in NAMD for estimation of the relative residence time (τ) of a protein-small molecule complex can be found [[https://kbbox.h-its.org/toolbox/tutorials/estimation-of-relative-residence-times-of-protein-ligand-complexes-using-random-acceleration-molecular-dynamics-ramd-implementation-in-namd/|here.]] | ||
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| + | === Implementation in GROMACS === | ||
| + | A tutorial describing the τRAMD process of setting up and running RAMD simulations in GROMACS for estimation of the relative residence time (τ) of a protein-small molecule complex can be found [[https://kbbox.h-its.org/toolbox/tutorials/estimation-of-relative-residence-times-of-protein-ligand-complexes-using-random-acceleration-molecular-dynamics-ramd-implementation-in-gromacs/|here]]. | ||
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| + | === τRAMD === | ||
| + | τ-random acceleration molecular dynamics (τRAMD) is a protocol based on the RAMD method for the ranking of drug candidates by their residence time and obtaining insights into ligand-target dissociation mechanism. An introduction to the method is given [[https://youtu.be/kCUyQtoo4cE|here]] | ||
