{"id":44596,"date":"2021-11-04T12:09:29","date_gmt":"2021-11-04T11:09:29","guid":{"rendered":"https:\/\/www.h-its.org\/de\/?p=44596"},"modified":"2021-11-05T10:16:03","modified_gmt":"2021-11-05T09:16:03","slug":"ramd","status":"publish","type":"post","link":"https:\/\/www.h-its.org\/de\/2021\/11\/04\/ramd\/","title":{"rendered":"\u03c4RAMD – Berechnung von Protein-Ligand-Dissoziationsraten und Erforschung von Dissoziationsmechanismen"},"content":{"rendered":"\n

Forscher\/-innen der Molecular and Cellular Modeling (MCM)<\/a> Gruppe am HITS haben \u03c4RAMD (\u03c4-Random Acceleration Molecular Dynamics) entwickelt: ein effizienter Workflow, der die Vorhersage relativer Wirkstoff-Protein-Verweilzeiten und die Analyse von Dissoziationsmechanismen auf automatisierte Weise erm\u00f6glicht. Als solches ist \u03c4RAMD ein flexibles Werkzeug, das in Arbeitsabl\u00e4ufe des rationalen Wirkstoffdesigns zum Entwurf neuer Molek\u00fcle oder zur Ligandenoptimierung implementiert werden kann.<\/p>\n\n\n\n

Das \u03c4RAMD-Protokoll<\/a> wendet RAMD an, um den Austritt eines kleinen Molek\u00fcls aus einem Zielrezeptor durch die Anwendung einer adaptiven, zuf\u00e4llig orientierten Kraft auf den Liganden zu beschleunigen. Der Workflow erm\u00f6glicht auch die Untersuchung von Dissoziationsmechanismen und die Charakterisierung von \u00dcbergangszust\u00e4nden durch das MD-IFP<\/a> (Molecular Dynamics – Interaction Fingerprint) Post-Analyse-Tool.<\/p>\n\n\n\n

Zus\u00e4tzlich zu den Implementierungen in den Softwarepaketen NAMD und AMBER <\/a>wurde \u03c4RAMD auch in die frei verf\u00fcgbare molekulare Simulationsmaschine GROMACS<\/a> f\u00fcr Simulationen auf CPU- oder GPU-Knoten implementiert.<\/p>\n\n\n\n

<\/div>\n\n\n\n
\"\"
Illustration der Anwendung des \u03c4RAMD- und MD-IFP-Workflows zur Simulation der Dissoziation einer wirkstoff\u00e4hnlichen Verbindung eines Zielproteins. Die Verbindung kann \u00fcber einen von drei Hauptpfaden dissoziieren, entlang derer verschiedene \u00dcbergangszust\u00e4nde abgetastet werden, die die Dissoziationsrate vom Protein beeinflussen.<\/figcaption><\/figure>\n\n\n\n
<\/div>\n\n\n\n

Weitere Quellen:<\/strong><\/p>\n\n\n\n

Kokh DB, Doser B, Richter S, Ormersbach F, Cheng X, Wade RC (2020). A workflow for exploring ligand dissociation from a macromolecule: Efficient random acceleration molecular dynamics simulation and interaction fingerprint analysis of ligand trajectories<\/a>, J. Chem. Phys. 153(12):125102<\/p>\n\n\n\n

Kokh DB, Amaral M, Bomke J, Gr\u00e4dler U, Musil D, Buchstaller H, Dreyer MK, Frech M, Lowinski M, VKokh DB, Amaral M, Bomke J, Gr\u00e4dler U, Musil D, Buchstaller H, Dreyer MK, Frech M, Lowinski M, Vallee F, Bianciotto M, Rak A, Wade RC (2018). Estimation of Drug-Target Residence Times by \u03c4-Random Acceleration Molecular Dynamics Simulations<\/a>, J. Chem. Theory Comput. 14(7):3859-3869<\/p>\n","protected":false},"excerpt":{"rendered":"

Forscher\/-innen der Molecular and Cellular Modeling (MCM) Gruppe am HITS haben \u03c4RAMD (\u03c4-Random Acceleration Molecular Dynamics) entwickelt: ein effizienter Workflow, …<\/p>\n","protected":false},"author":6,"featured_media":44597,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"inline_featured_image":false,"footnotes":""},"categories":[1421],"hits-research-group":[],"class_list":["post-44596","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-software-news"],"acf":[],"yoast_head":"\n\u03c4RAMD - Berechnung von Protein-Ligand-Dissoziationsraten und Erforschung von Dissoziationsmechanismen - HITS gGmbH<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.h-its.org\/de\/2021\/11\/04\/ramd\/\" \/>\n<meta property=\"og:locale\" content=\"de_DE\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"\u03c4RAMD - 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