{"id":5636,"date":"2020-04-07T16:21:56","date_gmt":"2020-04-07T15:21:56","guid":{"rendered":"https:\/\/www.blopig.com\/blog\/?p=5636"},"modified":"2020-04-07T16:25:39","modified_gmt":"2020-04-07T15:25:39","slug":"delinker","status":"publish","type":"post","link":"https:\/\/www.blopig.com\/blog\/2020\/04\/delinker\/","title":{"rendered":"DeLinker &#8211; Deep Generative Models for 3D Linker Design"},"content":{"rendered":"\n<p>*** Disclaimer: This blog post represents some shameless self-promotion. ***<\/p>\n\n\n\n<p>I am delighted to announce that our most recent work, DeLinker, was recently published in the Journal of Chemical Information and Modeling (<a href=\"https:\/\/doi.org\/10.1021\/acs.jcim.9b01120\">link<\/a>).<\/p>\n\n\n\n<figure class=\"wp-block-image size-large\"><img data-recalc-dims=\"1\" decoding=\"async\" loading=\"lazy\" src=\"https:\/\/i0.wp.com\/github.com\/oxpig\/DeLinker\/blob\/master\/DeLinker.png?w=625&#038;ssl=1\" alt=\"\" \/><\/figure>\n\n\n\n<!--more-->\n\n\n\n<p>DeLinker is a deep learning method based on graph neural networks that proposes linkers between molecular fragments. Crucially, DeLinker is a first step at incorporating 3D structural knowledge directly into the generation process. <\/p>\n\n\n\n<p>In our paper, we showed the application of DeLinker to fragment linking, scaffold hopping, and PROTAC design, and demonstrated substantial outperformance over a database baseline. <\/p>\n\n\n\n<p>We have open-sourced the code on GitHub (<a href=\"https:\/\/github.com\/oxpig\/DeLinker\">link<\/a>) and welcome any feedback and suggestions.<\/p>\n\n\n\n<p>We are currently working on extending DeLinker to new design problems, and improving our model. We also hope to release additional examples of a simplified workflow to make using our method more accessible.<\/p>\n\n\n\n<p>If you like our work or found it helpful, you can cite it as:<br>Imrie F, Bradley AR, van der Schaar M, Deane CM. Deep Generative Models for 3D Linker Design. Journal of Chemical Information and Modeling. 2020<br><br>BibTex:<br><code>@Article{Imrie2020,<br>author={Imrie, Fergus and Bradley, Anthony R. and van der Schaar, Mihaela and Deane, Charlotte M.},<br>title={Deep Generative Models for 3D Linker Design},<br>journal={Journal of Chemical Information and Modeling},<br>year={2020},<br>month={Mar},<br>day={20},<br>publisher={American Chemical Society},<br>issn={1549-9596},<br>doi={10.1021\/acs.jcim.9b01120},<br>url={https:\/\/doi.org\/10.1021\/acs.jcim.9b01120}<br>}<\/code><\/p>\n","protected":false},"excerpt":{"rendered":"<p>*** Disclaimer: This blog post represents some shameless self-promotion. *** I am delighted to announce that our most recent work, DeLinker, was recently published in the Journal of Chemical Information and Modeling (link).<\/p>\n","protected":false},"author":50,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"nf_dc_page":"","wikipediapreview_detectlinks":true,"_monsterinsights_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"ngg_post_thumbnail":0,"_jetpack_memberships_contains_paid_content":false,"footnotes":""},"categories":[187,189,48,201],"tags":[],"ppma_author":[535],"class_list":["post-5636","post","type-post","status-publish","format-standard","hentry","category-cheminformatics","category-machine-learning","category-publication","category-small-molecules"],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"authors":[{"term_id":535,"user_id":50,"is_guest":0,"slug":"fergus2","display_name":"Fergus Imrie","avatar_url":"https:\/\/secure.gravatar.com\/avatar\/19c18fa7f4d0a2aecc5f69760c6a9f2fc9b493dfe45b1fd333ccb447db9d6a90?s=96&d=mm&r=g","0":null,"1":"","2":"","3":"","4":"","5":"","6":"","7":"","8":""}],"_links":{"self":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/5636","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/users\/50"}],"replies":[{"embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/comments?post=5636"}],"version-history":[{"count":5,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/5636\/revisions"}],"predecessor-version":[{"id":5643,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/5636\/revisions\/5643"}],"wp:attachment":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/media?parent=5636"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/categories?post=5636"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/tags?post=5636"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/ppma_author?post=5636"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}