{"id":6,"date":"2025-10-01T12:03:03","date_gmt":"2025-10-01T10:03:03","guid":{"rendered":"https:\/\/www.ub.edu\/cadrugdesign\/?page_id=6"},"modified":"2025-10-01T12:03:03","modified_gmt":"2025-10-01T10:03:03","slug":"home","status":"publish","type":"page","link":"https:\/\/www.ub.edu\/cadrugdesign\/","title":{"rendered":"Home"},"content":{"rendered":"\n<h2 class=\"wp-block-heading\">Research Lines<\/h2>\n\n\n\n<h3 class=\"wp-block-heading\">Mollecular Modeling<\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">Structure-based design and discovery of protein ligands has emerged as a new tool in medicinal chemistry. In particular, the knowledge of the three-dimensional structure of a protein can be used to derive new protein ligands with improved binding properties ( i.e. new drugs ). Within this approach we need algorithms and methods to solve the following questions: What is the binding affinity of a novel ligand towards a particular receptor? What are the best conformations of a ligand to the binding site? What are the similarities of different ligands with respect to their recognition capabilities? With which orientation will a ligand bind to the active site? We want to contribute to obtain new answers for these questions and in particular for some problems concerning CANCER disease.<\/p>\n\n\n\n<h4 class=\"wp-block-heading\"><strong>Molecular Dynamics<\/strong><\/h4>\n\n\n\n<p class=\"wp-block-paragraph\">We apply molecular dynamics (MD) extensively using the AMBER and GROMACS suite of programs. MD is used to simulate the stability of protein dimers and of drug-protein complexes throughout time. We apply MD also to analyze the binding free energy of these complexes, employing the MMPBSA approximation.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Research Lines Mollecular Modeling Structure-based design and discovery of protein ligands has emerged as a new tool in medicinal chemistry.<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-6","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/www.ub.edu\/cadrugdesign\/wp-json\/wp\/v2\/pages\/6","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ub.edu\/cadrugdesign\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.ub.edu\/cadrugdesign\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.ub.edu\/cadrugdesign\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ub.edu\/cadrugdesign\/wp-json\/wp\/v2\/comments?post=6"}],"version-history":[{"count":1,"href":"https:\/\/www.ub.edu\/cadrugdesign\/wp-json\/wp\/v2\/pages\/6\/revisions"}],"predecessor-version":[{"id":8,"href":"https:\/\/www.ub.edu\/cadrugdesign\/wp-json\/wp\/v2\/pages\/6\/revisions\/8"}],"wp:attachment":[{"href":"https:\/\/www.ub.edu\/cadrugdesign\/wp-json\/wp\/v2\/media?parent=6"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}