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projects:tauramddescription [2020/07/21 08:55] richter |
projects:tauramddescription [2020/07/21 14:51] wade [Tutorial on application of RAMD] |
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=====References===== | =====References===== | ||
+ | ====RAMD and its applications (using the implementation in Gromacs) are described in:==== | ||
+ | * 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. **arXiv** 2020 [[https://arxiv.org/abs/2006.11066| arXiv:2006.11066]] | ||
====RAMD and its applications (using the implementation in NAMD) are described in:==== | ====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 [[https://pubs.acs.org/doi/10.1021/acs.jctc.8b00230|DOI: 10.1021/acs.jctc.8b00230]] | + | * 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]] |
- | * 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]] | + | * 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]] |
+ | * 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]] | ||
* 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]] | * 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]] | ||
* 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]] | * 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]] | ||
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=== Implementation in NAMD === | === Implementation in NAMD === | ||
- | A tutorial describing the <a href="https://www.h-its.org/downloads/ramd/" target="_blank" rel="noreferrer noopener">τRAMD</a> process of setting up and running RAMD simulations in NAMD for estimation of the relative residence time (τ) of a protein-small molecule complex can be found <a href="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/" target="_blank" rel="noreferrer noopener">here.</a> | + | 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.]] |
=== Implementation in GROMACS === | === Implementation in GROMACS === | ||
- | A tutorial describing the <a href="https://github.com/HITS-MCM/gromacs-ramd" target="_blank" rel="noreferrer noopener">τRAMD</a> 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 <a href="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/" target="_blank" rel="noreferrer noopener">here.</a> | + | 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 === | === 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 is given [[https://youtu.be/kCUyQtoo4cE|here]] | |
- | <p>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.</p> | + | |
- | [["https://www.h-its.org/downloads/ramd/|Read more]] | + | |