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| projects:tauramddescription [2024/07/17 15:44] – [Key Information and References for RAMD and tauRAMD] wade | projects:tauramddescription [2024/07/17 16:13] (current) – [RAMD and its applications (using the implementation in Gromacs) are described in:] wade |
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| For implementations of RAMD, versions are available for [[https://github.com/HITS-MCM/gromacs-ramd|GROMACS]], [[https://www.h-its.org/downloads/ramd/|NAMD]], [[https://ambermd.org/|AMBER]] and [[https://github.com/seekrcentral/openmm_ramd|OpenMM]]. | For implementations of RAMD, versions are available for [[https://github.com/HITS-MCM/gromacs-ramd|GROMACS]], [[https://www.h-its.org/downloads/ramd/|NAMD]], [[https://ambermd.org/|AMBER]] and [[https://github.com/seekrcentral/openmm_ramd|OpenMM]]. |
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| In addition, scripts for [[https://github.com/HITS-MCM/tauRAMD|tauRAMD]] and [[https://github.com/HITS-MCM/MD-IFP |analysis with MD-IFP (Molecular Dynamics Interaction FingerPrints]] 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:==== |
| * * 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]] | * 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]] |
| * * 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]] | * 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]] |
| * * Flores-León, C.D., Colorado-Pablo, L.F., Santos-Contreras, M.Á. and Aguayo-Ortiz, R., Determination of nucleoside DOT1L inhibitors’ residence times by τRAMD simulations. Frontiers in Drug Discovery, 2, p.1083198. (2023). [[https://doi.org/10.3389/fddsv.2022.1083198]] | * 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]] |
| * * Maximova, E., Postnikov, E.B., Lavrova, A.I., Farafonov, V. and Nerukh, D., Protein–ligand dissociation rate constant from all-atom simulation. The Journal of Physical Chemistry Letters, 12(43), pp.10631-10636. (2021). [[https://doi.org/10.1021/acs.jpclett.1c02952]] | * Flores-León, C.D., Colorado-Pablo, L.F., Santos-Contreras, M.Á. and Aguayo-Ortiz, R., Determination of nucleoside DOT1L inhibitors’ residence times by τRAMD simulations. Frontiers in Drug Discovery, 2, p.1083198. (2023). [[https://doi.org/10.3389/fddsv.2022.1083198]] |
| * * Kokh, D.B. and Wade, R.C., G protein-coupled receptor–ligand dissociation rates and mechanisms from τRAMD simulations. Journal of Chemical Theory and Computation, 17(10), pp.6610-6623. (2021). [[https://doi.org/10.1021/acs.jctc.1c00641]] | * Maximova, E., Postnikov, E.B., Lavrova, A.I., Farafonov, V. and Nerukh, D., Protein–ligand dissociation rate constant from all-atom simulation. The Journal of Physical Chemistry Letters, 12(43), pp.10631-10636. (2021). [[https://doi.org/10.1021/acs.jpclett.1c02952]] |
| | * Kokh, D.B. and Wade, R.C., G protein-coupled receptor–ligand dissociation rates and mechanisms from τRAMD simulations. Journal of Chemical Theory and Computation, 17(10), pp.6610-6623. (2021). [[https://doi.org/10.1021/acs.jctc.1c00641]] |
| * 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]] | * 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]] |
| ====RAMD and its applications (using the implementation in NAMD) are described in:==== | ====RAMD and its applications (using the implementation in NAMD) are described in:==== |
| * * Tan, S., Wang, J., Gao, P., Xie, G., Zhang, Q., Liu, H. and Yao, X., Unveiling the Selectivity Mechanism of Type-I LRRK2 Inhibitors by Computational Methods: Insights from Binding Thermodynamics and Kinetics Simulation. ACS Chemical Neuroscience, 14(18), pp.3472-3486. (2023). [[https://doi.org/10.1021/acschemneuro.3c00338]] | * Tan, S., Wang, J., Gao, P., Xie, G., Zhang, Q., Liu, H. and Yao, X., Unveiling the Selectivity Mechanism of Type-I LRRK2 Inhibitors by Computational Methods: Insights from Binding Thermodynamics and Kinetics Simulation. ACS Chemical Neuroscience, 14(18), pp.3472-3486. (2023). [[https://doi.org/10.1021/acschemneuro.3c00338]] |
| * * Tang, R., Wang, Z., Xiang, S., Wang, L., Yu, Y., Wang, Q., Deng, Q., Hou, T. and Sun, H., Uncovering the Kinetic Characteristics and Degradation Preference of PROTAC Systems with Advanced Theoretical Analyses. JACS Au, 3(6), pp.1775-1789. (2023). [[https://doi.org/10.1021/jacsau.3c00195]] | * Tang, R., Wang, Z., Xiang, S., Wang, L., Yu, Y., Wang, Q., Deng, Q., Hou, T. and Sun, H., Uncovering the Kinetic Characteristics and Degradation Preference of PROTAC Systems with Advanced Theoretical Analyses. JACS Au, 3(6), pp.1775-1789. (2023). [[https://doi.org/10.1021/jacsau.3c00195]] |
| * * Zhang, Q., Han, J., Zhu, Y., Tan, S. and Liu, H., Binding thermodynamics and dissociation kinetics analysis uncover the key structural motifs of phenoxyphenol derivatives as the direct InhA inhibitors and the hotspot residues of InhA. International Journal of Molecular Sciences, 23(17), p.10102. (2022). [[https://doi.org/10.3390/ijms231710102]] | * Zhang, Q., Han, J., Zhu, Y., Tan, S. and Liu, H., Binding thermodynamics and dissociation kinetics analysis uncover the key structural motifs of phenoxyphenol derivatives as the direct InhA inhibitors and the hotspot residues of InhA. International Journal of Molecular Sciences, 23(17), p.10102. (2022). [[https://doi.org/10.3390/ijms231710102]] |
| * * Berger, B. T., Amaral, M., Kokh, D. B., Nunes-Alves, A., Musil, D., Heinrich, T., ... and Knapp, S. Structure-kinetic relationship reveals the mechanism of selectivity of FAK inhibitors over PYK2. Cell Chemical Biology, 28(5), 686-698. (2021). [[https://doi.org/10.1016/j.chembiol.2021.01.003]] | * Berger, B. T., Amaral, M., Kokh, D. B., Nunes-Alves, A., Musil, D., Heinrich, T., ... and Knapp, S. Structure-kinetic relationship reveals the mechanism of selectivity of FAK inhibitors over PYK2. Cell Chemical Biology, 28(5), 686-698. (2021). [[https://doi.org/10.1016/j.chembiol.2021.01.003]] |
| * * 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]] |
| * * 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. 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]] |
| * 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]] |
| * * Wells, G., Yuan, H., McDaniel, M.J., Kusumoto, H., Snyder, J.P., Liotta, D.C. and Traynelis, S.F., The GluN2B‐Glu413Gly NMDA receptor variant arising from a de novo GRIN2B mutation promotes ligand‐unbinding and domain opening. Proteins: Structure, Function, and Bioinformatics, 86(12), pp.1265-1276. (2018). [[https://doi.org/10.1021/acs.jctc.8b01270]] | * Wells, G., Yuan, H., McDaniel, M.J., Kusumoto, H., Snyder, J.P., Liotta, D.C. and Traynelis, S.F., The GluN2B‐Glu413Gly NMDA receptor variant arising from a de novo GRIN2B mutation promotes ligand‐unbinding and domain opening. Proteins: Structure, Function, and Bioinformatics, 86(12), pp.1265-1276. (2018). [[https://doi.org/10.1002/prot.25595]] |
| * * Wells, G., Yuan, H., McDaniel, M.J., Kusumoto, H., Snyder, J.P., Liotta, D.C. and Traynelis, S.F., The GluN2B‐Glu413Gly NMDA receptor variant arising from a de novo GRIN2B mutation promotes ligand‐unbinding and domain opening. Proteins: Structure, Function, and Bioinformatics, 86(12), pp.1265-1276. (2018). [[https://doi.org/10.1002/prot.25595]] | * Du, J., Liu, L., Guo, L.Z., Yao, X.J. and Yang, J.M., Molecular basis of P450 OleT JE: an investigation of substrate binding mechanism and major pathways. Journal of Computer-Aided Molecular Design, 31, pp.483-495. (2017). [[https://doi.org/10.1007/s10822-017-0013-x]] |
| * * Du, J., Liu, L., Guo, L.Z., Yao, X.J. and Yang, J.M., Molecular basis of P450 OleT JE: an investigation of substrate binding mechanism and major pathways. Journal of Computer-Aided Molecular Design, 31, pp.483-495. (2017). [[https://doi.org/10.1007/s10822-017-0013-x]] | * Zhao, Y., She, N., Zhang, X., Wang, C. and Mo, Y., Product release mechanism and the complete enzyme catalysis cycle in yeast cytosine deaminase (yCD): A computational study. Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics, 1865(8), pp.1020-1029. (2017). [[https://doi.org/10.1016/j.bbapap.2017.05.001]] |
| * * Zhao, Y., She, N., Zhang, X., Wang, C. and Mo, Y., Product release mechanism and the complete enzyme catalysis cycle in yeast cytosine deaminase (yCD): A computational study. Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics, 1865(8), pp.1020-1029. (2017). [[https://doi.org/10.1016/j.bbapap.2017.05.001]] | * Pietra, F., On Dioxygen and Substrate Access to Soluble Methane Monooxygenases: An all‐Atom Molecular Dynamics Investigation in Water Solution. Chemistry & Biodiversity, 14(1), p.e1600158. (2017). [[https://doi.org/10.1002/cbdv.201600158]] |
| * * Pietra, F., On Dioxygen and Substrate Access to Soluble Methane Monooxygenases: An all‐Atom Molecular Dynamics Investigation in Water Solution. Chemistry & Biodiversity, 14(1), p.e1600158. (2017). [[https://doi.org/10.1002/cbdv.201600158]] | |
| * 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]] |
| * * Liu, Y., Tu, G., Lai, X., Kuang, B. and Li, S., Exploring ligand dissociation pathways from aminopeptidase N using random acceleration molecular dynamics simulation. Journal of molecular modeling, 22, pp.1-7. (2016). [[https://doi.org/10.1007/s00894-016-3105-y]] | * Liu, Y., Tu, G., Lai, X., Kuang, B. and Li, S., Exploring ligand dissociation pathways from aminopeptidase N using random acceleration molecular dynamics simulation. Journal of molecular modeling, 22, pp.1-7. (2016). [[https://doi.org/10.1007/s00894-016-3105-y]] |
| * * Lopata, A., Leveles, I., Bendes, Á.Á., Viskolcz, B., Vértessy, B.G., Jójárt, B. and Tóth, J., A hidden active site in the potential drug target mycobacterium tuberculosis dUTPase is accessible through small amplitude protein conformational changes. Journal of Biological Chemistry, 291(51), pp.26320-26331. (2016). [[https://doi.org/10.1074/jbc.M116.734012]] | * Lopata, A., Leveles, I., Bendes, Á.Á., Viskolcz, B., Vértessy, B.G., Jójárt, B. and Tóth, J., A hidden active site in the potential drug target mycobacterium tuberculosis dUTPase is accessible through small amplitude protein conformational changes. Journal of Biological Chemistry, 291(51), pp.26320-26331. (2016). [[https://doi.org/10.1074/jbc.M116.734012]] |
| * * Chen, N., Zhao, Y., Lu, J., Wu, R. and Cao, Z., Mechanistic insights into the rate-limiting step in purine-specific nucleoside hydrolase. Journal of Chemical Theory and Computation, 11(7), pp.3180-3188. (2016). [[https://doi.org/10.1021/acs.jctc.5b00045]] | * Chen, N., Zhao, Y., Lu, J., Wu, R. and Cao, Z., Mechanistic insights into the rate-limiting step in purine-specific nucleoside hydrolase. Journal of Chemical Theory and Computation, 11(7), pp.3180-3188. (2016). [[https://doi.org/10.1021/acs.jctc.5b00045]] |
| * * Cai, J., Li, J., Zhang, J., Ding, S., Liu, G., Li, W. and Tang, Y., Computational insights into inhibitory mechanism of azole compounds against human aromatase. RSC advances, 5(110), pp.90871-90880. (2015). [[https://doi.org/10.1039/C5RA24952J]] | * Cai, J., Li, J., Zhang, J., Ding, S., Liu, G., Li, W. and Tang, Y., Computational insights into inhibitory mechanism of azole compounds against human aromatase. RSC advances, 5(110), pp.90871-90880. (2015). [[https://doi.org/10.1039/C5RA24952J]] |
| * * Shang, Y., LeRouzic, V., Schneider, S., Bisignano, P., Pasternak, G.W. and Filizola, M., Mechanistic insights into the allosteric modulation of opioid receptors by sodium ions. Biochemistry, 53(31), pp.5140-5149. (2014). [[https://doi.org/10.1021/bi5006915]] | * Shang, Y., LeRouzic, V., Schneider, S., Bisignano, P., Pasternak, G.W. and Filizola, M., Mechanistic insights into the allosteric modulation of opioid receptors by sodium ions. Biochemistry, 53(31), pp.5140-5149. (2014). [[https://doi.org/10.1021/bi5006915]] |
| * * Pietra, F., Binding Pockets and Permeation Channels for Dioxygen through Cofactorless 3‐Hydroxy‐2‐methylquinolin‐4‐one 2, 4‐Dioxygenase in Association with Its Natural Substrate, 3‐Hydroxy‐2‐methylquinolin‐4 (1H)‐one. A Perspective from Molecular Dynamics Simulations. Chemistry & Biodiversity, 11(6), pp.861-871. (2014). [[https://doi.org/10.1002/cbdv.201400054]] | * Pietra, F., Binding Pockets and Permeation Channels for Dioxygen through Cofactorless 3‐Hydroxy‐2‐methylquinolin‐4‐one 2, 4‐Dioxygenase in Association with Its Natural Substrate, 3‐Hydroxy‐2‐methylquinolin‐4 (1H)‐one. A Perspective from Molecular Dynamics Simulations. Chemistry & Biodiversity, 11(6), pp.861-871. (2014). [[https://doi.org/10.1002/cbdv.201400054]] |
| * * Zhuang, S., Bao, L., Linhananta, A. and Liu, W., Molecular modeling revealed that ligand dissociation from thyroid hormone receptors is affected by receptor heterodimerization. Journal of Molecular Graphics and Modelling, 44, pp.155-160. (2013). [[https://doi.org/10.1016/j.jmgm.2013.06.001]] | * Zhuang, S., Bao, L., Linhananta, A. and Liu, W., Molecular modeling revealed that ligand dissociation from thyroid hormone receptors is affected by receptor heterodimerization. Journal of Molecular Graphics and Modelling, 44, pp.155-160. (2013). [[https://doi.org/10.1016/j.jmgm.2013.06.001]] |
| * * Pietra, F., On the pathways of biologically relevant diatomic gases through proteins. Dioxygen and heme oxygenase from the perspective of molecular dynamics. Chemistry & Biodiversity, 10(4), pp.556-568. (2013). [[https://doi.org/10.1002/cbdv.201200434]] | * Pietra, F., On the pathways of biologically relevant diatomic gases through proteins. Dioxygen and heme oxygenase from the perspective of molecular dynamics. Chemistry & Biodiversity, 10(4), pp.556-568. (2013). [[https://doi.org/10.1002/cbdv.201200434]] |
| * * Mirza, I.A., Burk, D.L., Xiong, B., Iwaki, H., Hasegawa, Y., Grosse, S., Lau, P.C. and Berghuis, A.M., Structural analysis of a novel cyclohexylamine oxidase from Brevibacterium oxydans IH-35A. PloS one, 8(3), p.e60072. (2013). [[https://doi.org/10.1371/journal.pone.0060072]] | * Mirza, I.A., Burk, D.L., Xiong, B., Iwaki, H., Hasegawa, Y., Grosse, S., Lau, P.C. and Berghuis, A.M., Structural analysis of a novel cyclohexylamine oxidase from Brevibacterium oxydans IH-35A. PloS one, 8(3), p.e60072. (2013). [[https://doi.org/10.1371/journal.pone.0060072]] |
| * 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]] |
| * * Merchant, B. A., and Madura, J. D. Insights from molecular dynamics: the binding site of cocaine in the dopamine transporter and permeation pathways of substrates in the leucine and dopamine transporters. Journal of Molecular Graphics and Modelling, 38, 1-12. (2012). [[https://doi.org/10.1016/j.jmgm.2012.05.007]] | * Merchant, B. A., and Madura, J. D. Insights from molecular dynamics: the binding site of cocaine in the dopamine transporter and permeation pathways of substrates in the leucine and dopamine transporters. Journal of Molecular Graphics and Modelling, 38, 1-12. (2012). [[https://doi.org/10.1016/j.jmgm.2012.05.007]] |
| * * Kalyaanamoorthy, S., and Chen, Y. P. P. Exploring inhibitor release pathways in histone deacetylases using random acceleration molecular dynamics simulations. Journal of chemical information and modeling, 52(2), 589-603. (2012). [[https://doi.org/10.1021/ci200584f]] | * Kalyaanamoorthy, S., and Chen, Y. P. P. Exploring inhibitor release pathways in histone deacetylases using random acceleration molecular dynamics simulations. Journal of chemical information and modeling, 52(2), 589-603. (2012). [[https://doi.org/10.1021/ci200584f]] |
| * * Yu, R., Kaas, Q. and Craik, D.J., Delineation of the unbinding pathway of α-conotoxin ImI from the α7 nicotinic acetylcholine receptor. The Journal of Physical Chemistry B, 116(21), pp.6097-6105. (2012). [[https://doi.org/10.1021/jp301352d]] | * Yu, R., Kaas, Q. and Craik, D.J., Delineation of the unbinding pathway of α-conotoxin ImI from the α7 nicotinic acetylcholine receptor. The Journal of Physical Chemistry B, 116(21), pp.6097-6105. (2012). [[https://doi.org/10.1021/jp301352d]] |
| * * Pietra, F. Molecular‐Dynamics Simulation of Dioxygen Egress from 12/15‐Lipoxygenase Arachidonic Acid Complex. Chemistry & Biodiversity, 9(6), 1019-1032. (2012). [[https://doi.org/10.1002/cbdv.201100305]] | * Pietra, F. Molecular‐Dynamics Simulation of Dioxygen Egress from 12/15‐Lipoxygenase Arachidonic Acid Complex. Chemistry & Biodiversity, 9(6), 1019-1032. (2012). [[https://doi.org/10.1002/cbdv.201100305]] |
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| =====Tutorials on the application of RAMD===== | |
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| === Implementation in NAMD === | |
| 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.]] | |
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| === Implementation in GROMACS === | |
| 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]]. | |
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| === 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. An introduction to the method is given [[https://youtu.be/kCUyQtoo4cE|here]] | |
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