{"id":405,"date":"2021-10-16T19:01:24","date_gmt":"2021-10-16T23:01:24","guid":{"rendered":"https:\/\/sites.temple.edu\/voelzlab\/?p=405"},"modified":"2021-10-16T19:01:25","modified_gmt":"2021-10-16T23:01:25","slug":"congrats-to-si-on-new-jctc-paper","status":"publish","type":"post","link":"https:\/\/sites.temple.edu\/voelzlab\/2021\/10\/16\/congrats-to-si-on-new-jctc-paper\/","title":{"rendered":"Congrats to Si on new JCTC paper"},"content":{"rendered":"\n

Congrats to graduate student Si Zhang on the publication of her first-author manuscript in JCTC<\/a>!<\/p>\n\n\n\n

This work was a collaboration with David Hahn (Janssen Research) of Open Force Field<\/a> fame, and Michael R. Shirts<\/a> (University of Colorado-Boulder) who originated and implemented this expanded ensemble (EE) method in GROMACS<\/a>. <\/p>\n\n\n\n

We were turned on to the EE approach during our work with the COVID Moonshot<\/a>, where we used CPU clients on
Folding@home<\/a> to screen 50k+ potential SARS-CoV-2 main protease (Mpro) inhibitors by their estimated absolute binding free energy (ABFE). <\/p>\n\n\n\n

Si realized that no one had yet applied this approach to calculating relative free energies. So she tested it for a set of 24 transformations between 16 Tyk2 inhibitors using the OpenFF “Parsely” small-molecule force field, and it worked very well, achieving an accuracy within 0.66 kcal\/mol (MUE) of the experimental value! Another result that portends well for using EE on distributed computing platforms like Folding@home: Performing N<\/em> independent simulations gives better accuracy than a single simulation N<\/em> times as long.<\/p>\n\n\n\n

You can read all about the details in our hot-off-the-press paper:<\/p>\n\n\n\n

Zhang, Si, David F. Hahn, Michael R. Shirts, and Vincent A. Voelz. \u201cExpanded Ensemble Methods Can Be Used to Accurately Predict Protein-Ligand Relative Binding Free Energies.\u201d Journal of Chemical Theory and Computation<\/em> 17, no. 10 (October 12, 2021): 6536\u201347. https:\/\/doi.org\/10.1021\/acs.jctc.1c00513<\/a>.<\/p>\n","protected":false},"excerpt":{"rendered":"

Congrats to graduate student Si Zhang on the publication of her first-author manuscript in JCTC! This work was a collaboration with David Hahn (Janssen Research) of Open Force Field fame, and Michael R. Shirts (University of Colorado-Boulder) who originated and implemented this expanded ensemble (EE) method in GROMACS. We were turned on to the EE … <\/p>\n

Continue reading “Congrats to Si on new JCTC paper”<\/span><\/a><\/p>\n","protected":false},"author":1258,"featured_media":0,"comment_status":"open","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":["post-405","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"_links":{"self":[{"href":"https:\/\/sites.temple.edu\/voelzlab\/wp-json\/wp\/v2\/posts\/405","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/sites.temple.edu\/voelzlab\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/sites.temple.edu\/voelzlab\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/sites.temple.edu\/voelzlab\/wp-json\/wp\/v2\/users\/1258"}],"replies":[{"embeddable":true,"href":"https:\/\/sites.temple.edu\/voelzlab\/wp-json\/wp\/v2\/comments?post=405"}],"version-history":[{"count":0,"href":"https:\/\/sites.temple.edu\/voelzlab\/wp-json\/wp\/v2\/posts\/405\/revisions"}],"wp:attachment":[{"href":"https:\/\/sites.temple.edu\/voelzlab\/wp-json\/wp\/v2\/media?parent=405"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/sites.temple.edu\/voelzlab\/wp-json\/wp\/v2\/categories?post=405"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/sites.temple.edu\/voelzlab\/wp-json\/wp\/v2\/tags?post=405"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}