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projects:tauramddescription [2020/07/21 14:51] wade [Tutorial on application of RAMD] |
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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| =====References===== | =====References===== | ||
| ====RAMD and its applications (using the implementation in Gromacs) are described in:==== | ====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]] | + | * 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]] |
| ====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. 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]] | * 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]] | ||
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| - | =====Tutorial on application of RAMD===== | + | =====Tutorials on the application of RAMD===== |
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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]] | + | 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]] |
