{"id":999,"date":"2020-10-26T10:51:25","date_gmt":"2020-10-26T10:51:25","guid":{"rendered":"http:\/\/serranolab.crg.eu\/?p=999"},"modified":"2020-10-26T10:57:28","modified_gmt":"2020-10-26T10:57:28","slug":"proteinfishing-a-protein-complex-generator-within-the-modelx-toolsuite","status":"publish","type":"post","link":"http:\/\/serranolab.crg.eu\/index.php\/2020\/10\/26\/proteinfishing-a-protein-complex-generator-within-the-modelx-toolsuite\/","title":{"rendered":"ProteinFishing: a protein complex generator within the ModelX toolsuite"},"content":{"rendered":"<p>Abstract:<br \/>\n&#8220;Accurate 3D modelling of protein-protein interactions (PPI) is essential to compensate for the absence of experimentally determined complex structures. Here, we present a new set of commands within the ModelX toolsuite capable of generating atomic-level protein complexes suitable for interface design. Among these commands, the new tool ProteinFishing proposes known and\/or putative alternative 3D PPI for a given protein complex. The algorithm exploits backbone compatibility of protein fragments to generate mutually exclusive protein interfaces that are quickly evaluated with a knowledge-based statistical force field. Using interleukin-10-R2 co-crystalized with interferon-lambda-3, and a database of X-ray structures containing interleukin-10, this algorithm was able to generate interleukin-10-R2\/interleukin-10 structural models in agreement with experimental data.&#8221;<\/p>\n<p>Read the <a href=\"https:\/\/academic.oup.com\/bioinformatics\/article\/36\/14\/4208\/5841655\">full text article<\/a>.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Abstract: &#8220;Accurate 3D modelling of protein-protein interactions (PPI) is essential to compensate for the absence of experimentally determined complex structures. Here, we present a new set of commands within the ModelX toolsuite capable of generating atomic-level protein complexes suitable for interface design. Among these commands, the new tool ProteinFishing proposes &hellip;<\/p>\n","protected":false},"author":11,"featured_media":1000,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_mi_skip_tracking":false},"categories":[15],"tags":[20,36,21],"_links":{"self":[{"href":"http:\/\/serranolab.crg.eu\/index.php\/wp-json\/wp\/v2\/posts\/999"}],"collection":[{"href":"http:\/\/serranolab.crg.eu\/index.php\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/serranolab.crg.eu\/index.php\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/serranolab.crg.eu\/index.php\/wp-json\/wp\/v2\/users\/11"}],"replies":[{"embeddable":true,"href":"http:\/\/serranolab.crg.eu\/index.php\/wp-json\/wp\/v2\/comments?post=999"}],"version-history":[{"count":3,"href":"http:\/\/serranolab.crg.eu\/index.php\/wp-json\/wp\/v2\/posts\/999\/revisions"}],"predecessor-version":[{"id":1011,"href":"http:\/\/serranolab.crg.eu\/index.php\/wp-json\/wp\/v2\/posts\/999\/revisions\/1011"}],"wp:featuredmedia":[{"embeddable":true,"href":"http:\/\/serranolab.crg.eu\/index.php\/wp-json\/wp\/v2\/media\/1000"}],"wp:attachment":[{"href":"http:\/\/serranolab.crg.eu\/index.php\/wp-json\/wp\/v2\/media?parent=999"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/serranolab.crg.eu\/index.php\/wp-json\/wp\/v2\/categories?post=999"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/serranolab.crg.eu\/index.php\/wp-json\/wp\/v2\/tags?post=999"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}