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projects:tauramddescription [2024/07/17 16:08] – [RAMD and its applications (using the implementation in NAMD) are described in:] wadeprojects:tauramddescription [2026/06/17 10:20] (current) – [Key Information and References for RAMD and tauRAMD] 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. 
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 +The listing of references given here is incomplete.
 ====RAMD and its applications (using the implementation in Gromacs) are described in:==== ====RAMD and its applications (using the implementation in Gromacs) are described in:====
 +  * D’Arrigo, G., Kokh, D.B., Nunes-Alves, A., Wade, R.C. (2024). Computational screening of the effects of mutations on protein-protein off-rates and dissociation mechanisms by τRAMD, Commun Biol 7(1):1159.[[https://doi.org/10.1038/s42003-024-06880-5]]
 +  * Paiardi, G., Ferraz, M., Rusnati, M., Wade, R.C. (2024). The accomplices: Heparan sulfates and N-glycans foster SARS-CoV-2 spike:ACE2 receptor binding and virus priming, Proc. Natl. Acad. Sci. U.S.A. 121(43):e240489212. [[https://doi.org/10.1073/pnas.2404892121]]
 +  * 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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