{"id":77,"date":"2021-06-14T08:05:54","date_gmt":"2021-06-14T07:05:54","guid":{"rendered":"https:\/\/modsim-pharma.com\/?page_id=77"},"modified":"2021-09-28T09:14:38","modified_gmt":"2021-09-28T08:14:38","slug":"qresfep","status":"publish","type":"page","link":"https:\/\/modsim-pharma.com\/index.php\/qresfep\/","title":{"rendered":"QresFEP"},"content":{"rendered":"\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-9d6595d7 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-vertically-aligned-center is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:200%\">\n<p><em>In silico mutagenesis with free energy perturbation (FEP) simulations<\/em>.<\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:33.33%\">\n<div class=\"wp-block-image\"><figure class=\"alignright size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"431\" height=\"429\" src=\"https:\/\/modsim-pharma.com\/wp-content\/uploads\/2021\/09\/QresFEP-HR-crop.png\" alt=\"\" class=\"wp-image-774\" srcset=\"https:\/\/modsim-pharma.com\/wp-content\/uploads\/2021\/09\/QresFEP-HR-crop.png 431w, https:\/\/modsim-pharma.com\/wp-content\/uploads\/2021\/09\/QresFEP-HR-crop-300x300.png 300w, https:\/\/modsim-pharma.com\/wp-content\/uploads\/2021\/09\/QresFEP-HR-crop-150x150.png 150w\" sizes=\"auto, (max-width: 431px) 100vw, 431px\" \/><\/figure><\/div>\n<\/div>\n<\/div>\n\n\n\n<p class=\"has-text-align-left\">QresFEP is based on a smooth annihilation protocol to perturb the aminoacid sidechain of interest. This protocol showed high convergence and robustness. <\/p>\n\n\n\n<p class=\"has-text-align-left\">The approach has been tested on multiple targets to estimate the effect of single point mutations on protein-ligand binding affinity, thermal stability or conformational equilibrium. QresFEP showed a consistent strong signal for predicting these effects. <\/p>\n\n\n\n<p class=\"has-text-align-left\">QresFEP is a flexible approach which can handle different forcefields and sampling options. The approach is fast and accurate, owing to the spherical boundary MD simulations within our Q package.<\/p>\n\n\n\n<div class=\"wp-block-image\"><figure class=\"aligncenter size-large is-resized\"><img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/modsim-pharma.com\/wp-content\/uploads\/2021\/07\/TOC_draft1-1024x414.png\" alt=\"\" class=\"wp-image-400\" width=\"819\" height=\"331\" srcset=\"https:\/\/modsim-pharma.com\/wp-content\/uploads\/2021\/07\/TOC_draft1-1024x414.png 1024w, https:\/\/modsim-pharma.com\/wp-content\/uploads\/2021\/07\/TOC_draft1-300x121.png 300w, https:\/\/modsim-pharma.com\/wp-content\/uploads\/2021\/07\/TOC_draft1-768x311.png 768w, https:\/\/modsim-pharma.com\/wp-content\/uploads\/2021\/07\/TOC_draft1-1536x621.png 1536w, https:\/\/modsim-pharma.com\/wp-content\/uploads\/2021\/07\/TOC_draft1-2048x828.png 2048w\" sizes=\"auto, (max-width: 819px) 100vw, 819px\" \/><\/figure><\/div>\n\n\n\n<p class=\"has-text-align-left\"><a rel=\"noreferrer noopener\" href=\"https:\/\/pubs.acs.org\/doi\/abs\/10.1021\/acs.jctc.9b00538\" target=\"_blank\">QresFEP: an automated protocol for free energy calculations of protein mutations in Q<\/a> <br>W. Jespers, G.V. Isaksen, T.A.H. Andberg, S. Vasile, A. van Veen, J. \u00c5qvist, B.O. Brandsdal, H. Guti\u00e9rrez-de-Ter\u00e1n, <em>Journal of Chemical Theory and Computation<\/em>&nbsp;<strong>2019<\/strong>, <em>15<\/em> (10), 5461\u20135473.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>In silico mutagenesis with free energy perturbation (FEP) simulations. QresFEP is based on a smooth annihilation protocol to perturb the aminoacid sidechain of interest. This protocol showed high convergence and robustness. The approach has been tested on multiple targets to estimate the effect of single point mutations on protein-ligand binding affinity, thermal stability or conformational&hellip;&nbsp;<a href=\"https:\/\/modsim-pharma.com\/index.php\/qresfep\/\" rel=\"bookmark\">Read More &raquo;<span class=\"screen-reader-text\">QresFEP<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"neve_meta_sidebar":"","neve_meta_container":"","neve_meta_enable_content_width":"","neve_meta_content_width":0,"neve_meta_title_alignment":"","neve_meta_author_avatar":"","neve_post_elements_order":"","neve_meta_disable_header":"","neve_meta_disable_footer":"","neve_meta_disable_title":"","footnotes":""},"class_list":["post-77","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/modsim-pharma.com\/index.php\/wp-json\/wp\/v2\/pages\/77","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/modsim-pharma.com\/index.php\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/modsim-pharma.com\/index.php\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/modsim-pharma.com\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/modsim-pharma.com\/index.php\/wp-json\/wp\/v2\/comments?post=77"}],"version-history":[{"count":16,"href":"https:\/\/modsim-pharma.com\/index.php\/wp-json\/wp\/v2\/pages\/77\/revisions"}],"predecessor-version":[{"id":775,"href":"https:\/\/modsim-pharma.com\/index.php\/wp-json\/wp\/v2\/pages\/77\/revisions\/775"}],"wp:attachment":[{"href":"https:\/\/modsim-pharma.com\/index.php\/wp-json\/wp\/v2\/media?parent=77"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}