{"id":2863,"date":"2023-06-14T10:09:29","date_gmt":"2023-06-14T09:09:29","guid":{"rendered":"https:\/\/archive.belbi.bg.ac.rs\/2023\/?post_type=abstract&#038;p=2863"},"modified":"2023-06-14T18:37:23","modified_gmt":"2023-06-14T17:37:23","slug":"comparative-study-of-in-silico-protein-design-techniques","status":"publish","type":"abstract","link":"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/comparative-study-of-in-silico-protein-design-techniques\/","title":{"rendered":"Comparative study of in silico protein design techniques"},"content":{"rendered":"\n<p>Ivan Tanasijevi\u0107<sup>1*<\/sup>, Branka Raki\u0107<sup>1<\/sup><\/p>\n\n\n\n<p class=\"affiliation-para\"><sup>1<\/sup>Institute for Artificial Intelligence R&amp;D, Fruskogorska 1, 21000 Novi Sad, Serbia<\/p>\n\n\n\n<p>ivan.tanasijevic [at] ivi.ac.rs<\/p>\n\n\n\n<p><strong>Abstract<\/strong><\/p>\n\n\n\n<p class=\"abstract-para\">Protein design plays a pivotal role in various scientific and industrial applications, such as drug development and biotechnology. With the advancement of computational methods, new tools and algorithms have emerged to facilitate the generation of novel protein designs. This study presents a comparative analysis of Pepspec and RFdiffusion, two prominent methods in protein design, to evaluate their effectiveness in designing peptides with desired properties. Mainly, we aim to design peptides that bind with high affinity and specificity to a desired protein target.<\/p>\n\n\n\n<p class=\"abstract-para\">Pepspec is an application native to the Rosetta software package. It relies on Monte Carlo sampling of backbone confirmations and residue mutations and a stochastic optimization based on the Rosetta score \u2013 a measure approximating the binding free-energy of the complex.  <\/p>\n\n\n\n<p class=\"abstract-para\">On the other hand, a recently developed tool, RFdiffusion, is a denoising diffusion probabilistic model based on an existing artificial neural network, RoseTTAFold, developed for protein structure estimation. It is trained to remove noise from protein structures on a large database of protein complexes to ultimately be able to generate novel binder designs based on the target structure. <\/p>\n\n\n\n<p class=\"abstract-para\">In this study, we aim to compare the efficiency of these two design tools. As it is common in generative ML algorithms, the comparison will be made by evaluating both the design quality and design versatility. The quality will be assessed by using the well-known AlphaFold2 Machine learning tool to estimate the binding affinity of the peptide-protein complex while the versatility will be measured using standard sequence based statistical methods. <\/p>\n\n\n\n<p class=\"abstract-para\">RFdiffusion and Pepspec offer distinct approaches to protein design. By assessing the strengths and limitations of each method in this study, we aim to deepen the understanding of these methods and allow leveraging these tools effectively in designing peptides with desired characteristics, contributing to advancements in the field of protein engineering and biotechnology.<\/p>\n\n\n\n<p class=\"abstract-para\"><strong>Keywords:<\/strong> Rational protein design, AI\/ML in biology and medicine, Computational bioengineering  <\/p>\n","protected":false},"excerpt":{"rendered":"<p>Ivan Tanasijevi\u0107<sup>1*<\/sup>, Branka Raki\u0107<sup>1<\/sup><\/p>\n<p class=\"affiliation-para\"><sup>1<\/sup>Institute for Artificial Intelligence R&amp;D, Fruskogorska 1, 21000 Novi Sad, Serbia<\/p>\n<p> <a class=\"continue-reading-link\" href=\"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/comparative-study-of-in-silico-protein-design-techniques\/\"><span>Continue reading<\/span><i class=\"crycon-right-dir\"><\/i><\/a> <\/p>\n","protected":false},"author":162,"featured_media":0,"template":"","categories":[8],"tags":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v23.0 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Comparative study of in silico protein design techniques - BelBi 2023<\/title>\n<meta name=\"robots\" content=\"noindex, follow\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Comparative study of in silico protein design techniques - BelBi 2023\" \/>\n<meta property=\"og:description\" content=\"Ivan Tanasijevi\u01071*, Branka Raki\u010711Institute for Artificial Intelligence R&amp;D, Fruskogorska 1, 21000 Novi Sad, Serbia Continue reading\" \/>\n<meta property=\"og:url\" content=\"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/comparative-study-of-in-silico-protein-design-techniques\/\" \/>\n<meta property=\"og:site_name\" content=\"BelBi 2023\" \/>\n<meta property=\"article:modified_time\" content=\"2023-06-14T17:37:23+00:00\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"WebPage\",\"@id\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/comparative-study-of-in-silico-protein-design-techniques\/\",\"url\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/comparative-study-of-in-silico-protein-design-techniques\/\",\"name\":\"Comparative study of in silico protein design techniques - BelBi 2023\",\"isPartOf\":{\"@id\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/#website\"},\"datePublished\":\"2023-06-14T09:09:29+00:00\",\"dateModified\":\"2023-06-14T17:37:23+00:00\",\"breadcrumb\":{\"@id\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/comparative-study-of-in-silico-protein-design-techniques\/#breadcrumb\"},\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"ReadAction\",\"target\":[\"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/comparative-study-of-in-silico-protein-design-techniques\/\"]}]},{\"@type\":\"BreadcrumbList\",\"@id\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/comparative-study-of-in-silico-protein-design-techniques\/#breadcrumb\",\"itemListElement\":[{\"@type\":\"ListItem\",\"position\":1,\"name\":\"Home\",\"item\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/\"},{\"@type\":\"ListItem\",\"position\":2,\"name\":\"Comparative study of in silico protein design techniques\"}]},{\"@type\":\"WebSite\",\"@id\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/#website\",\"url\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/\",\"name\":\"BelBi 2023\",\"description\":\"\",\"publisher\":{\"@id\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/#organization\"},\"potentialAction\":[{\"@type\":\"SearchAction\",\"target\":{\"@type\":\"EntryPoint\",\"urlTemplate\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/?s={search_term_string}\"},\"query-input\":\"required name=search_term_string\"}],\"inLanguage\":\"en-US\"},{\"@type\":\"Organization\",\"@id\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/#organization\",\"name\":\"Belgrade Bioinformatics Conference\",\"url\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/\",\"logo\":{\"@type\":\"ImageObject\",\"inLanguage\":\"en-US\",\"@id\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/#\/schema\/logo\/image\/\",\"url\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/wp-content\/uploads\/2023\/02\/145_97_171.png\",\"contentUrl\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/wp-content\/uploads\/2023\/02\/145_97_171.png\",\"width\":278,\"height\":500,\"caption\":\"Belgrade Bioinformatics Conference\"},\"image\":{\"@id\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/#\/schema\/logo\/image\/\"}}]}<\/script>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"Comparative study of in silico protein design techniques - BelBi 2023","robots":{"index":"noindex","follow":"follow"},"og_locale":"en_US","og_type":"article","og_title":"Comparative study of in silico protein design techniques - BelBi 2023","og_description":"Ivan Tanasijevi\u01071*, Branka Raki\u010711Institute for Artificial Intelligence R&amp;D, Fruskogorska 1, 21000 Novi Sad, Serbia Continue reading","og_url":"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/comparative-study-of-in-silico-protein-design-techniques\/","og_site_name":"BelBi 2023","article_modified_time":"2023-06-14T17:37:23+00:00","twitter_card":"summary_large_image","schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"WebPage","@id":"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/comparative-study-of-in-silico-protein-design-techniques\/","url":"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/comparative-study-of-in-silico-protein-design-techniques\/","name":"Comparative study of in silico protein design techniques - BelBi 2023","isPartOf":{"@id":"https:\/\/archive.belbi.bg.ac.rs\/2023\/#website"},"datePublished":"2023-06-14T09:09:29+00:00","dateModified":"2023-06-14T17:37:23+00:00","breadcrumb":{"@id":"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/comparative-study-of-in-silico-protein-design-techniques\/#breadcrumb"},"inLanguage":"en-US","potentialAction":[{"@type":"ReadAction","target":["https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/comparative-study-of-in-silico-protein-design-techniques\/"]}]},{"@type":"BreadcrumbList","@id":"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/comparative-study-of-in-silico-protein-design-techniques\/#breadcrumb","itemListElement":[{"@type":"ListItem","position":1,"name":"Home","item":"https:\/\/archive.belbi.bg.ac.rs\/2023\/"},{"@type":"ListItem","position":2,"name":"Comparative study of in silico protein design techniques"}]},{"@type":"WebSite","@id":"https:\/\/archive.belbi.bg.ac.rs\/2023\/#website","url":"https:\/\/archive.belbi.bg.ac.rs\/2023\/","name":"BelBi 2023","description":"","publisher":{"@id":"https:\/\/archive.belbi.bg.ac.rs\/2023\/#organization"},"potentialAction":[{"@type":"SearchAction","target":{"@type":"EntryPoint","urlTemplate":"https:\/\/archive.belbi.bg.ac.rs\/2023\/?s={search_term_string}"},"query-input":"required name=search_term_string"}],"inLanguage":"en-US"},{"@type":"Organization","@id":"https:\/\/archive.belbi.bg.ac.rs\/2023\/#organization","name":"Belgrade Bioinformatics Conference","url":"https:\/\/archive.belbi.bg.ac.rs\/2023\/","logo":{"@type":"ImageObject","inLanguage":"en-US","@id":"https:\/\/archive.belbi.bg.ac.rs\/2023\/#\/schema\/logo\/image\/","url":"https:\/\/archive.belbi.bg.ac.rs\/2023\/wp-content\/uploads\/2023\/02\/145_97_171.png","contentUrl":"https:\/\/archive.belbi.bg.ac.rs\/2023\/wp-content\/uploads\/2023\/02\/145_97_171.png","width":278,"height":500,"caption":"Belgrade Bioinformatics Conference"},"image":{"@id":"https:\/\/archive.belbi.bg.ac.rs\/2023\/#\/schema\/logo\/image\/"}}]}},"_links":{"self":[{"href":"https:\/\/archive.belbi.bg.ac.rs\/2023\/wp-json\/wp\/v2\/abstract\/2863"}],"collection":[{"href":"https:\/\/archive.belbi.bg.ac.rs\/2023\/wp-json\/wp\/v2\/abstract"}],"about":[{"href":"https:\/\/archive.belbi.bg.ac.rs\/2023\/wp-json\/wp\/v2\/types\/abstract"}],"author":[{"embeddable":true,"href":"https:\/\/archive.belbi.bg.ac.rs\/2023\/wp-json\/wp\/v2\/users\/162"}],"wp:attachment":[{"href":"https:\/\/archive.belbi.bg.ac.rs\/2023\/wp-json\/wp\/v2\/media?parent=2863"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/archive.belbi.bg.ac.rs\/2023\/wp-json\/wp\/v2\/categories?post=2863"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/archive.belbi.bg.ac.rs\/2023\/wp-json\/wp\/v2\/tags?post=2863"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}