{"id":1834,"date":"2017-07-16T10:18:18","date_gmt":"2017-07-16T10:18:18","guid":{"rendered":"https:\/\/www.mgms.org\/WordPress\/lecture-tour-2\/"},"modified":"2022-09-04T08:28:11","modified_gmt":"2022-09-04T08:28:11","slug":"lecture-tour-2020","status":"publish","type":"page","link":"https:\/\/www.mgms.org\/WordPress\/conferences\/lecture-tour-2020\/","title":{"rendered":"2020 MGMS Lecture Tour &#8211; Prof. Rebecca Wade"},"content":{"rendered":"<p><strong>All MGMS Seminars are free of charge and open to all.<\/strong><\/p>\n<p>The <a href=\"http:\/\/The MGMS organises around 3-6 meetings per year. They can range from one-day meetings on a specific topic, to multi-day international conferences on a broader subject, such as \u201cBiomolecular Simulations.\u201d Our community has a broad range of interests in the field of molecular simulations and graphics, including the modelling of biological systems, graphical representations of molecules, bio- and chemoinformatics, small molecule modelling, method developments, as well an interest in new computer architecture development.\" data-wplink-url-error=\"true\">MGMS was formed in 1981<\/a> to bring together scientists working in different fields of study\u2014such as chemistry, physics, biology, mathematics and computer science\u2014who have a common interest in computational molecular modelling and molecular graphics. One of our activities is to organize <em>MGMS Lecture Tours<\/em> to highlight cutting-edge research in the field.<\/p>\n<h3><strong>2020: Prof. Rebecca Wade<\/strong><\/h3>\n<figure style=\"width: 386px\" class=\"wp-caption aligncenter\"><img data-recalc-dims=\"1\" loading=\"lazy\" decoding=\"async\" class=\"size-thumbnail\" src=\"https:\/\/i0.wp.com\/www.zmbh.uni-heidelberg.de\/Wade\/images\/Wade_web.jpg?resize=386%2C468&#038;ssl=1\" alt=\"Prof. Rebecca Wade, ZMBH Research Group Leader, HITS (Heidelberg Institute for Theoretical Studies)\" width=\"386\" height=\"468\"><figcaption class=\"wp-caption-text\">Prof. Rebecca Wade<\/figcaption><\/figure>\n<p>We are pleased to announce that&nbsp;<a href=\"https:\/\/www.zmbh.uni-heidelberg.de\/Wade\/default.shtml\">Prof. Rebecca Wade<\/a>&nbsp;from Heidelberg Institute for Theoretical Studies (HITS) and Heidelberg University, Germany will be giving a virtual MGMS Lecture Tour lecture titled, <em>&#8220;Computational Approaches to Protein Dynamics and Binding Kinetics for Drug Discovery&#8221;<\/em>, and it will be held via <a href=\"https:\/\/us02web.zoom.us\/j\/89649417193?pwd=cGVTblBERElyTTFsVmhONTl3K015dz09\">Zoom<\/a> on:<\/p>\n<h4><strong>Tuesday, November 24<sup>th<\/sup>, 2020<\/strong><\/h4>\n<ul>\n<li><strong>2:00-2:45 pm GMT: &nbsp;Lecture: <em>&#8220;Computational Approaches to Protein Dynamics and Binding Kinetics for Drug Discovery&#8221;<\/em><\/strong><\/li>\n<li><strong>2:45- 3:00 pm GMT: Q&amp;A<\/strong><\/li>\n<li><strong>3:00 pm GMT: MGMS Annual General Meeting (AGM)<\/strong><\/li>\n<\/ul>\n<h2><strong>&#8220;Computational Approaches to Protein Dynamics and Binding Kinetics for Drug Discovery&#8221;<\/strong><\/h2>\n<h3>Rebecca C. Wade<sup>1<\/sup><sup>,2<\/sup>&nbsp;<\/h3>\n<ul style=\"list-style-type: square;\">\n<li><sup>1<\/sup>Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany,&nbsp;<\/li>\n<li><sup>2<\/sup>Zentrum f\u00fcr Molekulare Biologie (ZMBH), DKFZ-ZMBH Alliance and Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Germany&nbsp;<\/li>\n<\/ul>\n<p>The dynamic nature of protein structures and the diversity of protein binding pocket dynamics provide challenges and opportunities for ligand design [1]. I will present the recent development of a machine learning approach to identify pocket conformations with high druggability in TRAPP, a toolbox of computational approaches to identify TRAnsient Pockets in Proteins for ligand design (<a href=\"https:\/\/trapp.h-its.org\/\">https:\/\/trapp.h-its.org\/<\/a>). [2]. Protein binding site flexibility is one of the factors that can affect drug-target binding kinetics. Growing evidence that the efficacy of a drug can be correlated to target binding kinetics has led to the development of many new methods aimed at computing rate constants for receptor-ligand binding processes [3,4], see also: <a href=\"http:\/\/kbbox.h-its.org\/\">kbbox.h-its.org<\/a>. Here, I will describe our studies to explore the determinants of structure-kinetic relationships and to develop computationally efficient methods to estimate drug-target binding kinetic parameters. I will introduce the t-random acceleration molecular dynamics simulation (tRAMD) method to compute relative residence times [5] and discuss how interaction fingerprint (MD-IFP [6]) and machine learning analysis [7] of tRAMD trajectories can be used to decipher the determinants of drug-target residence times.&nbsp;<\/p>\n<p>Her lecture can be accessed <a href=\"https:\/\/www.youtube.com\/watch?v=QFbxeovFRtg&amp;t=101s\">here<\/a>.&nbsp;<\/p>\n<p><iframe loading=\"lazy\" title=\"YouTube video player\" src=\"https:\/\/www.youtube.com\/embed\/QFbxeovFRtg\" width=\"560\" height=\"315\" frameborder=\"0\" allowfullscreen=\"allowfullscreen\"><\/iframe><\/p>\n<p><\/p>\n<ul>\n<li>[1] Stank A, Kokh DB, Fuller JC, Wade RC. Protein binding pocket dynamics. <em>Acc. Chem Res.,<\/em> <strong>2016<\/strong>, 49:809-815. &nbsp;<\/li>\n<li>[2] Yuan JH, Han SB, Richter S, Wade RC, Kokh DB, Druggability Assessment in TRAPP using Machine Learning Approaches J. Chem. Inf. Model. <strong>2020<\/strong>, 60 (3), 1685-1699<\/li>\n<li>[3] Bruce NJ, Ganotra GK, Kokh DB, Sadiq SK, Wade RC. New approaches for computing ligand-receptor binding kinetics. <em>Curr Opin Struct Biol.<\/em> <strong>2018<\/strong>, 49: 1-10.<\/li>\n<li>[4] Nunes-Alves A, Kokh DB, Wade RC. Recent progress in molecular simulation methods for drug binding kinetics <em>Curr Opin Struct Biol. <\/em><strong>2020<\/strong>, 64:126-133.<\/li>\n<li>[5] Kokh DB, Amaral M,\u2026\u2026Wade RC.&nbsp; Estimation of drug-target residence times by t-random acceleration molecular dynamics simulations, <em>J. Chem. <\/em><em>Theory Comput.<\/em> <strong>2018<\/strong>, 14: 3859\u20133869.<\/li>\n<li>[6] Kokh DB, Doser B, Richter S, Ormersbach F, Cheng X, Wade RC, <strong>2020, <\/strong>arXiv:2006.11066<\/li>\n<li>[7] Kokh DB, Kaufmann T, Kister B, Wade RC.&nbsp; Machine Learning Analysis of tRAMD Trajectories to Decipher Molecular Determinants of Drug-Target Residence Times, <em>Frontiers. Mol. Biosci. <\/em>&nbsp;<strong>2019<\/strong>, 6: 36.<\/li>\n<\/ul>\n<p><strong>About Rebecca Wade<br><\/strong>&nbsp;<br><em>Rebecca Wade leads&nbsp;the Molecular and Cellular Modeling group&nbsp;at&nbsp;Heidelberg Institute for Theoretical Studies (HITS) and is Professor of Computational&nbsp;Structural&nbsp;Biology at the Center for Molecular Biology at Heidelberg University&nbsp;(ZMBH).&nbsp;&nbsp;Rebecca Wade studied at Oxford University and, following postdoctoral&nbsp;research at the&nbsp;universities of Houston and Illinois, became a group leader at&nbsp;the European Molecular Biology Laboratory (EMBL) in Heidelberg in 1992. She moved&nbsp;to HITS in&nbsp;2001.&nbsp;Rebecca Wade\u2019s&nbsp;research is focused on the development and application of computer-aided&nbsp;methods to model and simulate biomolecular interactions.&nbsp;Her&nbsp;research group has developed novel protein&nbsp;structure-based methods for drug discovery and protein engineering,&nbsp;most recently for studying drug binding kinetics,&nbsp;as&nbsp;well as multiresolution computational approaches to investigate macromolecular&nbsp;association and the effects of macromolecular crowding. Rebecca Wade\u2019s research&nbsp;has been published in over 250 scientific papers, as well as software programs&nbsp;and web servers that are used world-wide. She is an Associate Editor of the&nbsp;Journal&nbsp;of Molecular Recognition and PloS Computational Biology. She was the&nbsp;recipient of the 2004 Hansch Award of the QSAR and Modelling Society and the&nbsp;2016&nbsp;International Society of Quantum Biology and Pharmacology (ISQBP) Award in&nbsp;Computational Biology.&nbsp;&nbsp;URL:&nbsp;<a href=\"http:\/\/www.h-its.org\/mcm\">www.h-its.org\/mcm<\/a>.<\/em><\/p>\n<p>Prof. Wade, an alumna of the University of Oxford, is:<\/p>\n<ul>\n<li>Group leader of the&nbsp;<a href=\"http:\/\/www.h-its.org\/en\/research\/mcm\/\" data-fancybox-group=\"fb_gallery_0_0\">Molecular and Cellular Modeling (MCM)<\/a>&nbsp;group at HITS;<\/li>\n<li><a href=\"http:\/\/www.zmbh.uni-heidelberg.de\/Wade\/default.shtml\" target=\"_blank\" rel=\"noreferrer noopener\" data-fancybox-group=\"fb_gallery_0_0\">Professor<\/a>&nbsp;at the&nbsp;<a href=\"http:\/\/www.zmbh.uni-heidelberg.de\/\" target=\"_blank\" rel=\"noopener noreferrer\" data-fancybox-group=\"fb_gallery_0_0\">Zentrum f\u00fcr Molekulare Biologie&nbsp;<\/a><a href=\"http:\/\/www.zmbh.uni-heidelberg.de\/\" target=\"_blank\" rel=\"noreferrer noopener\" data-fancybox-group=\"fb_gallery_0_0\">(ZMBH)<\/a>,&nbsp;<a href=\"http:\/\/www.uni-heidelberg.de\/\" target=\"_blank\" rel=\"noreferrer noopener\" data-fancybox-group=\"fb_gallery_0_0\">Heidelberg University<\/a>;<\/li>\n<li><a href=\"http:\/\/www.dkfz-zmbh-allianz.de\/forschungsprogramme\/programm1-wade_en.html\" target=\"_blank\" rel=\"noopener noreferrer\" data-fancybox-group=\"fb_gallery_0_0\">Group leader<\/a>&nbsp;in the DKFZ-ZMBH Alliance; and<\/li>\n<li>Group leader at the&nbsp;<a href=\"http:\/\/www.iwr.uni-heidelberg.de\/\" target=\"_blank\" rel=\"noreferrer noopener\" data-fancybox-group=\"fb_gallery_0_0\">Interdisciplinary Center for Scientific Computing (IWR).<\/a><\/li>\n<\/ul>\n<p>You can read more about Prof. Wade&#8217;s&nbsp;<a href=\"https:\/\/www.h-its.org\/people\/prof-dr-rebecca-wade\/\">background<\/a> and <a href=\"https:\/\/www.h-its.org\/people\/prof-dr-rebecca-wade\/\">research interests<\/a>.<\/p>\n<h2>Past MGMS Lecture Tours<\/h2>\n<table style=\"width: 566px;\" border=\"0\" cellspacing=\"0\" cellpadding=\"10\" align=\"center\">\n<tbody>\n<tr>\n<td style=\"width: 58px;\">2018<\/td>\n<td style=\"width: 508px;\"><a href=\"http:\/\/www.bris.ac.uk\/chemistry\/people\/david-r-glowacki\/index.html\">Dr. David Glowacki<\/a>,<br>University of Bristol, UK<\/td>\n<\/tr>\n<tr>\n<td style=\"width: 58px;\">2015<\/td>\n<td style=\"width: 508px;\"><a href=\"https:\/\/www.mgms.org\/lecture_tour.html\" target=\"_blank\" rel=\"noopener noreferrer\">Professor Dr Gisbert Schneider<\/a>,<br>ETH Zurich, Switzerland<\/td>\n<\/tr>\n<tr>\n<td style=\"width: 58px;\">2014<\/td>\n<td style=\"width: 508px;\"><a href=\"http:\/\/www.mgms.org\/lecture_tour\/lecture_tour_2014.html\">Prof. Arthur J. Olson<\/a>,<br>The Scripps Research Institute, La Jolla, California, USA<\/td>\n<\/tr>\n<tr>\n<td style=\"width: 58px;\">2012<\/td>\n<td style=\"width: 508px;\"><a href=\"http:\/\/www.mgms.org\/lecture_tour\/lecture_tour_2012.html\">Prof. Modesto Orozco<\/a>,<br>Group Leader, Molecular Modelling and Bioinformatics, Institute for Research in Biomedicine (IRB Barcelona)<\/td>\n<\/tr>\n<tr>\n<td style=\"width: 58px;\">2011<\/td>\n<td style=\"width: 508px;\"><a href=\"http:\/\/www.mgms.org\/lecture_tour\/lecture_tour_2011.html\">Prof. Tim Clark<\/a>,<br>Friedrich-Alexander-University Erlangen- Nurnberg, Germany, and<br>Centre for Molecular Design, University of Portsmouth<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n\n","protected":false},"excerpt":{"rendered":"<p>This is just a short excerpt for the about&nbsp;page.<\/p>\n","protected":false},"author":2,"featured_media":0,"parent":114,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"pmpro_default_level":"","jetpack_post_was_ever_published":false,"footnotes":""},"tags":[45,46],"class_list":["post-1834","page","type-page","status-publish","hentry","tag-mgms-lecture-tour","tag-postponed","pmpro-has-access","without-featured-image"],"jetpack_sharing_enabled":true,"jetpack_shortlink":"https:\/\/wp.me\/P91jzT-tA","_links":{"self":[{"href":"https:\/\/www.mgms.org\/WordPress\/wp-json\/wp\/v2\/pages\/1834","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.mgms.org\/WordPress\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.mgms.org\/WordPress\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.mgms.org\/WordPress\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/www.mgms.org\/WordPress\/wp-json\/wp\/v2\/comments?post=1834"}],"version-history":[{"count":3,"href":"https:\/\/www.mgms.org\/WordPress\/wp-json\/wp\/v2\/pages\/1834\/revisions"}],"predecessor-version":[{"id":1860,"href":"https:\/\/www.mgms.org\/WordPress\/wp-json\/wp\/v2\/pages\/1834\/revisions\/1860"}],"up":[{"embeddable":true,"href":"https:\/\/www.mgms.org\/WordPress\/wp-json\/wp\/v2\/pages\/114"}],"wp:attachment":[{"href":"https:\/\/www.mgms.org\/WordPress\/wp-json\/wp\/v2\/media?parent=1834"}],"wp:term":[{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.mgms.org\/WordPress\/wp-json\/wp\/v2\/tags?post=1834"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}