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projects:tauramddescription [2020/07/21 13:29] kokhadmin [RAMD and its applications (using the implementation in NAMD) are described in:] |
projects:tauramddescription [2020/07/21 13:30] kokhadmin [RAMD and its applications (using the implementation in NAMD) are described in:] |
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| * 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, **14**, 7, 3859–3869 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]] | ||
