Differences
This shows you the differences between two versions of the page.
| Both sides previous revision Previous revision Next revision | Previous revision Next revision Both sides next revision | ||
|
projects:tauramddescription [2020/07/21 13:30] kokhadmin [RAMD and its applications (using the implementation in NAMD) are described in:] |
projects:tauramddescription [2020/07/21 14:51] wade [Tutorial on application of RAMD] |
||
|---|---|---|---|
| Line 1: | Line 1: | ||
| =====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 | + | * 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]] |
| - | [[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]] | ||
| Line 31: | Line 30: | ||
| === Implementation in NAMD === | === Implementation in NAMD === | ||
| - | A tutorial describing the [[https://www.h-its.org/downloads/ramd/|τRAMD]] 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 ;[[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.]] | + | 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 [[https://github.com/HITS-MCM/gromacs-ramd|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]]. | + | 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]]. |
| | | ||
| === 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. [[https://www.h-its.org/downloads/ramd/|Read more]] | + | 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]] |
