{"id":2961,"date":"2016-03-17T10:30:31","date_gmt":"2016-03-17T10:30:31","guid":{"rendered":"http:\/\/www.blopig.com\/blog\/?p=2961"},"modified":"2016-12-13T16:12:37","modified_gmt":"2016-12-13T16:12:37","slug":"do-we-need-the-constant-regions-of-antibodies-and-t-cell-receptors-in-molecular-simulations","status":"publish","type":"post","link":"https:\/\/www.blopig.com\/blog\/2016\/03\/do-we-need-the-constant-regions-of-antibodies-and-t-cell-receptors-in-molecular-simulations\/","title":{"rendered":"Do we need the constant regions of Antibodies and T-cell receptors in molecular simulations?"},"content":{"rendered":"

At this week\u2019s journal club I presented my latest results on the effect of the constant regions of antibodies (ABs) and T-cell receptors (TCRs) on the dynamics of the overall system. Not including constant regions in such simulations is a commonly used simplification that is found throughout the literature. This is mainly due a massive saving in computational runtime as illustrated below: \"cutConstRegions\"<\/a><\/p>\n

The constant regions contain about 210 residues but an additional speed up comes from the much smaller solvation box. If a cubic solvation box is used then the effect is even more severe:<\/p>\n

\"waterbath\"<\/a>But the question is: “Is is OK to remove the constant regions of an AB or TCR and simulate without them?”.<\/p>\n

Using replica simulations we found that simulations with and without constant regions lead to (on average) significantly different results. The detail of our analysis will soon be submitted to a scientific journal. The current working title is \u201cWhy constant regions are essential in antibody and T-cell receptor Molecular Dynamics simulations\u201d.<\/p>\n","protected":false},"excerpt":{"rendered":"

At this week\u2019s journal club I presented my latest results on the effect of the constant regions of antibodies (ABs) and T-cell receptors (TCRs) on the dynamics of the overall system. Not including constant regions in such simulations is a commonly used simplification that is found throughout the literature. This is mainly due a massive […]<\/p>\n","protected":false},"author":17,"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":[10,138],"tags":[141,144,139,143,140,142],"ppma_author":[510],"class_list":["post-2961","post","type-post","status-publish","format-standard","hentry","category-groupmeetings","category-journal-club","tag-antibodies","tag-constant-regions","tag-molecular-dynamics","tag-replica-simulations","tag-tcrs","tag-water"],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"authors":[{"term_id":510,"user_id":17,"is_guest":0,"slug":"bernhard","display_name":"Bernhard Knapp","avatar_url":"https:\/\/secure.gravatar.com\/avatar\/53782f5b79941404d76518e10474992513623613fdcffc6f824091d49be3cff4?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\/2961","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\/17"}],"replies":[{"embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/comments?post=2961"}],"version-history":[{"count":2,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/2961\/revisions"}],"predecessor-version":[{"id":3240,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/2961\/revisions\/3240"}],"wp:attachment":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/media?parent=2961"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/categories?post=2961"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/tags?post=2961"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/ppma_author?post=2961"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}