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projects:tauramddescription [2024/07/17 15:58] – [RAMD and its applications (using the implementation in NAMD) are described in:] wadeprojects:tauramddescription [2024/07/17 16:13] (current) – [RAMD and its applications (using the implementation in Gromacs) are described in:] wade
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 In addition, scripts for  [[https://github.com/HITS-MCM/tauRAMD|tauRAMD]] and [[https://github.com/HITS-MCM/MD-IFP |MD-IFP (Interaction FingerPrint Analysis of Molecular Dynamics trajectories)]] are available.  In addition, scripts for  [[https://github.com/HITS-MCM/tauRAMD|tauRAMD]] and [[https://github.com/HITS-MCM/MD-IFP |MD-IFP (Interaction FingerPrint Analysis of Molecular Dynamics trajectories)]] are available. 
 ====RAMD and its applications (using the implementation in Gromacs) are described in:==== ====RAMD and its applications (using the implementation in Gromacs) are described in:====
 +  * Sohraby, F. and Nunes-Alves, A. Characterization of the Bottlenecks and Pathways for Inhibitor Dissociation from [NiFe] Hydrogenase Journal of Chemical Information and Modeling 2024 64 (10), 4193-4203. (2024).[[https://pubs.acs.org/doi/10.1021/acs.jcim.4c00187|https://doi.org/10.1021/acs.jcim.4c00187]]
   * de Oliveira, M.V.D., da Costa, K.S., Silva, J.R.A., Lameira, J. and Lima, A.H., Role of UDP‐N‐acetylmuramic acid in the regulation of MurA activity revealed by molecular dynamics simulations. Protein Science, 33(4), p.e4969. (2024). [[https://doi.org/10.1002/pro.4969]]   * de Oliveira, M.V.D., da Costa, K.S., Silva, J.R.A., Lameira, J. and Lima, A.H., Role of UDP‐N‐acetylmuramic acid in the regulation of MurA activity revealed by molecular dynamics simulations. Protein Science, 33(4), p.e4969. (2024). [[https://doi.org/10.1002/pro.4969]]
   * Maciel, L.G., Ferraz, M.V., Oliveira, A.A., Lins, R.D., Dos Anjos, J.V., Guido, R.V. and Soares, T.A., Inhibition of 3-Hydroxykynurenine Transaminase from Aedes aegypti and Anopheles gambiae: A mosquito-specific target to combat the transmission of arboviruses. ACS bio & med Chem Au, 3(2), pp.211-222. (2023). [[https://doi.org/10.1021/acsbiomedchemau.2c00080]]   * Maciel, L.G., Ferraz, M.V., Oliveira, A.A., Lins, R.D., Dos Anjos, J.V., Guido, R.V. and Soares, T.A., Inhibition of 3-Hydroxykynurenine Transaminase from Aedes aegypti and Anopheles gambiae: A mosquito-specific target to combat the transmission of arboviruses. ACS bio & med Chem Au, 3(2), pp.211-222. (2023). [[https://doi.org/10.1021/acsbiomedchemau.2c00080]]
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   * Nunes-Alves, A., Kokh, D.B. and Wade, R.C., Ligand unbinding mechanisms and kinetics for T4 lysozyme mutants from τRAMD simulations. Current Research in Structural Biology, 3, pp.106-111. (2021). [[https://doi.org/10.1016/j.crstbi.2021.04.001]]   * Nunes-Alves, A., Kokh, D.B. and Wade, R.C., Ligand unbinding mechanisms and kinetics for T4 lysozyme mutants from τRAMD simulations. Current Research in Structural Biology, 3, pp.106-111. (2021). [[https://doi.org/10.1016/j.crstbi.2021.04.001]]
   * Zhang, Z., Fan, F., Luo, W., Zhao, Y. and Wang, C., Molecular dynamics revealing a detour-forward release mechanism of tacrine: implication for the specific binding characteristics in butyrylcholinesterase. Frontiers in Chemistry, 8, p.730. (2020). [[https://doi.org/10.3389/fchem.2020.00730]]   * Zhang, Z., Fan, F., Luo, W., Zhao, Y. and Wang, C., Molecular dynamics revealing a detour-forward release mechanism of tacrine: implication for the specific binding characteristics in butyrylcholinesterase. Frontiers in Chemistry, 8, p.730. (2020). [[https://doi.org/10.3389/fchem.2020.00730]]
-  * Chaudhary, S.K., Iyyappan, Y., Elayappan, M., Jeyakanthan, J. and Sekar, K., Insights into product release dynamics through structural analyses of thymidylate kinase. International journal of biological macromolecules, 123, pp.637-647. [[https://doi.org/10.1016/j.ijbiomac.2018.11.025]] +  * Chaudhary, S.K., Iyyappan, Y., Elayappan, M., Jeyakanthan, J. and Sekar, K., Insights into product release dynamics through structural analyses of thymidylate kinase. International journal of biological macromolecules, 123, pp.637-647. (2019). [[https://doi.org/10.1016/j.ijbiomac.2018.11.025]] 
-  * 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]] +  * Bruno, A., Barresi, E., Simola,N., Da Pozzo, E., Costa, B., Novellino, E., Da Settimo, F., Martini, C., Taliani, S. and Cosconati, S. Unbinding of Translocator Protein 18 kDa (TSPO) Ligands: From in Vitro Residence Time to in Vivo Efficacy via in Silico Simulations.  ACS Chemical Neuroscience  10 (8), 3805-3814. (2019). [[https://pubs.acs.org/doi/10.1021/acschemneuro.9b00300|DOI: 10.1021/acschemneuro.9b00300]] 
 +  * 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]] 
   * Muvva, C., Murugan, N.A., Kumar Choutipalli, V.S. and Subramanian, V., Unraveling the unbinding pathways of products formed in catalytic reactions involved in SIRT1–3: A random acceleration molecular dynamics simulation study. Journal of Chemical Information and Modeling, 59(10), pp.4100-4115. (2019). [[https://doi.org/10.1021/acs.jcim.9b00513]]   * Muvva, C., Murugan, N.A., Kumar Choutipalli, V.S. and Subramanian, V., Unraveling the unbinding pathways of products formed in catalytic reactions involved in SIRT1–3: A random acceleration molecular dynamics simulation study. Journal of Chemical Information and Modeling, 59(10), pp.4100-4115. (2019). [[https://doi.org/10.1021/acs.jcim.9b00513]]
   * 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]]

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