{"id":63413,"date":"2008-10-03T00:00:00","date_gmt":"2008-10-03T00:00:00","guid":{"rendered":"https:\/\/www.deberes.net\/tesis\/sin-categoria\/evolutionary-algorithms-and-de-novo-peptide-design\/"},"modified":"2008-10-03T00:00:00","modified_gmt":"2008-10-03T00:00:00","slug":"evolutionary-algorithms-and-de-novo-peptide-design","status":"publish","type":"post","link":"https:\/\/www.deberes.net\/tesis\/peptidos\/evolutionary-algorithms-and-de-novo-peptide-design\/","title":{"rendered":"Evolutionary algorithms and de novo peptide design"},"content":{"rendered":"

Tesis doctoral de Ignacio Belda Reig <\/strong><\/h2>\n

The present thesis addresses the specific biomedical problem of the automated design of peptide ligands that bind therapeutic protein targets. To achieve this, we use evolutionary algorithms that evolve peptide populations. Evolutionary algorithms start the search with random peptides-individuals-, and then, by applying evolutionary rules-survival of fitness, genotypic inheritance, etc. -Explore the space in an implicitly parallel manner. The fitness function that determines the fitness of each individual-in other words, the function to be optimized-is the free energy of binding between the peptide ligand being evaluated and the target protein. This energy is obtained through peptide-protein docking simulations. in this thesis i study several implementations of evolutionary algorithms and some extensions that amplify evolutionary computational capacities, such as parallel evolutionary algorithms, multimodal evolutionary algorithms, fitness inheritance techniques, and variable length individuals evolution. Finally, the methodology-enpda (evolutionary de novo peptide design algorithm)-is applied to the design of peptides that can recognize biomedical important targets, such as, the proteins p53, prolyl oligopeptidase, dna gyrase, and mhc h-2kb, as well as a model of amyloid-\u00edY (1-42) fibril. among the developed and tested extensions of the evolutionary algorithms, there is the two-leveled parallelization performed on the evolutionary algorithms, with an almost linear scalability; the multimodal evolutionary algorithms developed, which lead the evolutionary process towards a molecular diverse search; the fitness inheritance techniques, that, theoretically, are expected to speed up in a great manner the evolutionary process, but it does not happen in enpda, due to the hypothesis explained later on; and the variable length individuals evolution, which prepares enpda to dynamically adapt peptide size to each protein surface patch. i also develop a data mining technolog<\/p>\n

 <\/p>\n

Datos acad\u00e9micos de la tesis doctoral \u00abEvolutionary algorithms and de novo peptide design<\/strong>\u00ab<\/h3>\n
    \n
  • T\u00edtulo de la tesis:<\/strong>\u00a0 Evolutionary algorithms and de novo peptide design <\/li>\n
  • Autor:<\/strong>\u00a0 Ignacio Belda Reig <\/li>\n
  • Universidad:<\/strong>\u00a0 Polit\u00e9cnica de catalunya<\/li>\n
  • Fecha de lectura de la tesis:<\/strong>\u00a0 10\/03\/2008<\/li>\n<\/ul>\n

     <\/p>\n

    Direcci\u00f3n y tribunal<\/h3>\n
      \n
    • Director de la tesis<\/strong>\n
        \n
      • Ernest Giralt Lledo<\/li>\n<\/ul>\n<\/li>\n
      • Tribunal<\/strong>\n
          \n
        • Presidente del tribunal: Juan Jes\u00fas Perez gonzalez <\/li>\n
        • natalio Krasnogor (vocal)<\/li>\n
        • xavier Messeguer peypoch (vocal)<\/li>\n
        • xavier Salvatella (vocal)<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n

           <\/p>\n","protected":false},"excerpt":{"rendered":"

          Tesis doctoral de Ignacio Belda Reig The present thesis addresses the specific biomedical problem of the automated design of peptide […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"site-sidebar-layout":"default","site-content-layout":"","ast-site-content-layout":"","site-content-style":"default","site-sidebar-style":"default","ast-global-header-display":"","ast-banner-title-visibility":"","ast-main-header-display":"","ast-hfb-above-header-display":"","ast-hfb-below-header-display":"","ast-hfb-mobile-header-display":"","site-post-title":"","ast-breadcrumbs-content":"","ast-featured-img":"","footer-sml-layout":"","theme-transparent-header-meta":"","adv-header-id-meta":"","stick-header-meta":"","header-above-stick-meta":"","header-main-stick-meta":"","header-below-stick-meta":"","astra-migrate-meta-layouts":"default","ast-page-background-enabled":"default","ast-page-background-meta":{"desktop":{"background-color":"var(--ast-global-color-4)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-gradient":""},"tablet":{"background-color":"","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-gradient":""},"mobile":{"background-color":"","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-gradient":""}},"ast-content-background-meta":{"desktop":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-gradient":""},"tablet":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-gradient":""},"mobile":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-gradient":""}},"footnotes":""},"categories":[15977,2528,969,15596],"tags":[1100,140018,15620,137886,78936,140019],"class_list":["post-63413","post","type-post","status-publish","format-standard","hentry","category-diseno-con-ayuda-de-ordenador","category-inteligencia-artificial","category-peptidos","category-politecnica-de-catalunya","tag-ernest-giralt-lledo","tag-ignacio-belda-reig","tag-juan-jesus-perez-gonzalez","tag-natalio-krasnogor","tag-xavier-messeguer-peypoch","tag-xavier-salvatella"],"_links":{"self":[{"href":"https:\/\/www.deberes.net\/tesis\/wp-json\/wp\/v2\/posts\/63413","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.deberes.net\/tesis\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.deberes.net\/tesis\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.deberes.net\/tesis\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.deberes.net\/tesis\/wp-json\/wp\/v2\/comments?post=63413"}],"version-history":[{"count":0,"href":"https:\/\/www.deberes.net\/tesis\/wp-json\/wp\/v2\/posts\/63413\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.deberes.net\/tesis\/wp-json\/wp\/v2\/media?parent=63413"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.deberes.net\/tesis\/wp-json\/wp\/v2\/categories?post=63413"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.deberes.net\/tesis\/wp-json\/wp\/v2\/tags?post=63413"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}