{"id":365,"date":"2024-10-20T12:45:42","date_gmt":"2024-10-20T11:45:42","guid":{"rendered":"https:\/\/hpcwithus.discoverer.bg\/?p=365"},"modified":"2024-10-27T09:38:20","modified_gmt":"2024-10-27T09:38:20","slug":"computed-on-discoverer-calculation-and-visualization-of-protein-conformations-generation-in-implicit-solvent","status":"publish","type":"post","link":"https:\/\/hpcwithus.discoverer.bg\/?p=365","title":{"rendered":"[Computed on Discoverer] Calculation and visualization of protein conformations generation in implicit solvent"},"content":{"rendered":"\n<p>We have numerous results we would like to share with you. One instance is the computation that demonstrates the conformation changes that make <a href=\"https:\/\/en.wikipedia.org\/wiki\/Protein_folding\" data-type=\"link\" data-id=\"https:\/\/en.wikipedia.org\/wiki\/Protein_folding\">the protein to fold and unfold<\/a>. The proper analysis of those changes help <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/20052756\/\" data-type=\"link\" data-id=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/20052756\/\">to measure the free energy<\/a> of different processes related to the protein chain transformations.<\/p>\n\n\n\n<p>Our protein model representation depicts the side chains of each residue by utilizing a<a href=\"https:\/\/pubs.acs.org\/doi\/10.1021\/acs.chemrev.6b00163\" data-type=\"link\" data-id=\"https:\/\/pubs.acs.org\/doi\/10.1021\/acs.chemrev.6b00163\"> coarse grain force field<\/a>, as illustrated in the video slides. By doing this, we significantly reduce the number of pair atom-atom interactions needed to compute the components of the potential energy and speed up the progress of the computations.<\/p>\n\n\n\n\n\n<p><\/p>\n","protected":false},"excerpt":{"rendered":"<p>We have numerous results we would like to share with you. One instance is the computation that demonstrates the conformation changes that make the protein to fold and unfold. The proper analysis of those changes help to measure the free energy of different processes related to the protein chain transformations. Our protein model representation depicts the side chains of each residue by utilizing a coarse grain force field, as illustrated in the video slides. By doing this, we significantly reduce&#8230;<\/p>\n<p class=\"read-more\"><a class=\"btn btn-default\" href=\"https:\/\/hpcwithus.discoverer.bg\/?p=365\"> Read More<span class=\"screen-reader-text\">  Read More<\/span><\/a><\/p>\n","protected":false},"author":2,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"saved_in_kubio":false,"footnotes":""},"categories":[75],"tags":[93,91,95,94,90,33,13,12,92],"class_list":["post-365","post","type-post","status-publish","format-standard","hentry","category-simulators","tag-coarse-grain","tag-conformations","tag-continuous-sampling","tag-force-field","tag-fortran-2008","tag-intel-oneapi-mkl","tag-llvm","tag-nvidia-hpc-sdk","tag-proteins"],"_links":{"self":[{"href":"https:\/\/hpcwithus.discoverer.bg\/index.php?rest_route=\/wp\/v2\/posts\/365","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/hpcwithus.discoverer.bg\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/hpcwithus.discoverer.bg\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/hpcwithus.discoverer.bg\/index.php?rest_route=\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/hpcwithus.discoverer.bg\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=365"}],"version-history":[{"count":4,"href":"https:\/\/hpcwithus.discoverer.bg\/index.php?rest_route=\/wp\/v2\/posts\/365\/revisions"}],"predecessor-version":[{"id":371,"href":"https:\/\/hpcwithus.discoverer.bg\/index.php?rest_route=\/wp\/v2\/posts\/365\/revisions\/371"}],"wp:attachment":[{"href":"https:\/\/hpcwithus.discoverer.bg\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=365"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/hpcwithus.discoverer.bg\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=365"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/hpcwithus.discoverer.bg\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=365"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}