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projects:tauramddescription [2020/07/21 13:28]
kokhadmin [RAMD and its applications (using the implementation in NAMD) are described in:]
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  +  * 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]] ​
-[[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]]  
-  * 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/​abs/​10.1021/​acs.jctc.8b00230|DOI:​ 10.1021/​acs.jctc.8b00230]]  +  * 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]]+  * 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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-=====Tutorial ​on application of RAMD=====+=====Tutorials ​on the application of RAMD=====
  
  
 === 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 to the method is given [[https://youtu.be/kCUyQtoo4cE|here]]
  
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