{"id":20,"date":"2024-09-16T12:32:14","date_gmt":"2024-09-16T15:32:14","guid":{"rendered":"http:\/\/ramirezlab.udec.cl\/?page_id=20"},"modified":"2025-01-24T16:10:40","modified_gmt":"2025-01-24T19:10:40","slug":"resources","status":"publish","type":"page","link":"http:\/\/ramirezlab.udec.cl\/es\/resources\/","title":{"rendered":"Resources"},"content":{"rendered":"<div data-elementor-type=\"wp-page\" data-elementor-id=\"20\" class=\"elementor elementor-20\" data-elementor-post-type=\"page\">\n\t\t\t\t<div class=\"elementor-element elementor-element-4011f85 e-con-full e-flex e-con e-parent\" data-id=\"4011f85\" data-element_type=\"container\">\n\t\t\t\t<div class=\"elementor-element elementor-element-4f017d7 elementor--h-position-center elementor--v-position-middle elementor-arrows-position-inside elementor-pagination-position-inside elementor-widget elementor-widget-slides\" data-id=\"4f017d7\" data-element_type=\"widget\" data-settings=\"{&quot;navigation&quot;:&quot;both&quot;,&quot;autoplay&quot;:&quot;yes&quot;,&quot;pause_on_hover&quot;:&quot;yes&quot;,&quot;pause_on_interaction&quot;:&quot;yes&quot;,&quot;autoplay_speed&quot;:5000,&quot;infinite&quot;:&quot;yes&quot;,&quot;transition&quot;:&quot;slide&quot;,&quot;transition_speed&quot;:500}\" data-widget_type=\"slides.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<div class=\"elementor-swiper\">\n\t\t\t\t\t<div class=\"elementor-slides-wrapper elementor-main-swiper swiper\" role=\"region\" aria-roledescription=\"carousel\" aria-label=\"Slides\" dir=\"ltr\" data-animation=\"fadeInUp\">\n\t\t\t\t<div class=\"swiper-wrapper elementor-slides\">\n\t\t\t\t\t\t\t\t\t\t<div class=\"elementor-repeater-item-84beeb1 swiper-slide\" role=\"group\" aria-roledescription=\"slide\"><div class=\"swiper-slide-bg\" role=\"img\"><\/div><div class=\"swiper-slide-inner\" ><div class=\"swiper-slide-contents\"><div class=\"elementor-slide-heading\">Resourses<\/div><div class=\"elementor-slide-description\">Pharmacoinformatics & Systems Pharmacology<\/div><\/div><\/div><\/div>\t\t\t\t<\/div>\n\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t<div class=\"elementor-element elementor-element-99020fa e-flex e-con-boxed e-con e-parent\" data-id=\"99020fa\" data-element_type=\"container\">\n\t\t\t\t\t<div class=\"e-con-inner\">\n\t\t\t\t<div class=\"elementor-element elementor-element-3140445 elementor-widget elementor-widget-text-editor\" data-id=\"3140445\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>Here you could find Tutorials, script library, gallery, FAQ, and a little bit more for pharmacoinformatics and drug design<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-c12278d elementor-widget elementor-widget-search\" data-id=\"c12278d\" data-element_type=\"widget\" data-settings=\"{&quot;submit_trigger&quot;:&quot;click_submit&quot;,&quot;pagination_type_options&quot;:&quot;none&quot;}\" data-widget_type=\"search.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<search class=\"e-search hidden\" role=\"search\">\n\t\t\t<form class=\"e-search-form\" action=\"\/es\/\" method=\"get\" data-trp-original-action=\"http:\/\/ramirezlab.udec.cl\/es\">\n\n\t\t\t\t\n\t\t\t\t<label class=\"e-search-label\" for=\"search-c12278d\">\n\t\t\t\t\t<span class=\"elementor-screen-only\">\n\t\t\t\t\t\tBuscar\t\t\t\t\t<\/span>\n\t\t\t\t\t\t\t\t\t<\/label>\n\n\t\t\t\t<div class=\"e-search-input-wrapper\">\n\t\t\t\t\t<input id=\"search-c12278d\" placeholder=\"Type to start searching...\" class=\"e-search-input\" type=\"search\" name=\"s\" value=\"\" autocomplete=\"off\" role=\"combobox\" aria-autocomplete=\"list\" aria-expanded=\"false\" aria-controls=\"results-c12278d\" aria-haspopup=\"listbox\">\n\t\t\t\t\t<svg aria-hidden=\"true\" class=\"e-font-icon-svg e-fas-times\" viewbox=\"0 0 352 512\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\"><path d=\"M242.72 256l100.07-100.07c12.28-12.28 12.28-32.19 0-44.48l-22.24-22.24c-12.28-12.28-32.19-12.28-44.48 0L176 189.28 75.93 89.21c-12.28-12.28-32.19-12.28-44.48 0L9.21 111.45c-12.28 12.28-12.28 32.19 0 44.48L109.28 256 9.21 356.07c-12.28 12.28-12.28 32.19 0 44.48l22.24 22.24c12.28 12.28 32.2 12.28 44.48 0L176 322.72l100.07 100.07c12.28 12.28 32.2 12.28 44.48 0l22.24-22.24c12.28-12.28 12.28-32.19 0-44.48L242.72 256z\"><\/path><\/svg>\t\t\t\t\t\t\t\t\t\t<output id=\"results-c12278d\" class=\"e-search-results-container hide-loader\" aria-live=\"polite\" aria-atomic=\"true\" aria-label=\"Resultados de b\u00fasqueda\" tabindex=\"0\">\n\t\t\t\t\t\t<div class=\"e-search-results\"><\/div>\n\t\t\t\t\t\t\t\t\t\t\t<\/output>\n\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t<button class=\"e-search-submit\" type=\"submit\">\n\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t\t<span class=\"\">\n\t\t\t\t\t\tBuscar\t\t\t\t\t<\/span>\n\t\t\t\t\t\t\t\t\t<\/button>\n\t\t\t\t<input type=\"hidden\" name=\"e_search_props\" value=\"c12278d-20\">\n\t\t\t<input type=\"hidden\" name=\"trp-form-language\" value=\"es\"\/><\/form>\n\t\t<\/search>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t<div class=\"elementor-element elementor-element-fcb4314 e-flex e-con-boxed e-con e-parent\" data-id=\"fcb4314\" data-element_type=\"container\">\n\t\t\t\t\t<div class=\"e-con-inner\">\n\t\t\t\t<div class=\"elementor-element elementor-element-4705de4 elementor-widget elementor-widget-text-editor\" data-id=\"4705de4\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<h2>Computational polypharmacology<\/h2><h3>Approved drugs from Drugbank<\/h3><p>DrugBank is a pharmaceutical knowledge database and a key pharmacoinformatics resource with comprehensive drug\/target\/disease information. In this notebook, we will download approved drugs information for Alzheimer\u00b4s Disease from DrugBank.<\/p><h3>Protein-protein interactions networks<\/h3><p>Here we use a KNIME workflow to capture relevant information related to an indication of interest involving a complete list of targets, drug names, and their respective study phase, and key protein-protein interactions. This workflow is fed with different databases such as CHEMBL, TTD, DRUGBANK, STRING and OPEN TARGETS, which contributes to the selection and prioritization of targets mapped and the identification of a new set of proteins as drug target candidates.<\/p><h3>Topological Protein-protein interactions networks analysis<\/h3><p>Here we present a R-Studio pipeline to compute some topological parameters that will help us understand the &#8220;importancy&#8221; of each protein in a PPI network in terms of its connections. Here we will use the PPI network for the Alzheimer&#8217;s disease (PPI-AD) obteined in our group using KNIME.<\/p><p>\u00a0<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-b76e001 elementor-widget-divider--view-line elementor-widget elementor-widget-divider\" data-id=\"b76e001\" data-element_type=\"widget\" data-widget_type=\"divider.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-divider\">\n\t\t\t<span class=\"elementor-divider-separator\">\n\t\t\t\t\t\t<\/span>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-bab23a9 elementor-widget elementor-widget-text-editor\" data-id=\"bab23a9\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<h2>Data Science with KNIME<\/h2><h3>Knime_tutorial<\/h3><p>In this tutorial, we will work a Knime introduction working with CHEMBL data using basic nodes.<\/p><h3>Chemoinformatics Analysis Tutorial with Knime master<\/h3><p>In this tutorial, we will work with the CHEMBL database and the open-source software KNIME, which will allow us to acquire the data of interest of the compounds that have been tested against a given target.<\/p><h3>Active compounds for a given target from ChEMBL<\/h3><p>This workflow use a local CHEMBL database to search one or a list of targets and return information of compounds and activity reported to the input targets.<\/p><h3>Chemoinformatics<\/h3><p>This workflow consists of 5 interconnected work blocks, each containing a central theme in computer-aided drug design (CADD). The workflow is presented using Acetylcholinesterase (AChE) as an example, including its respective active compounds and their respective associated IC50 values, which where obtained from CHEMBL database.<\/p><h3>Processing Pharmacophores from Phase<\/h3><p>Here we use a KNIME workflow to post-process the output file CSV from a multiple pharmacophore-based virtual screening calculation done with Phase. We screening a dataset of ~1000 compounds against multiple pharmacophores (~100), then the results were exported as a CSV file with all the results with the corresponding phase screen score (0 to 1).<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-11fd063 elementor-widget-divider--view-line elementor-widget elementor-widget-divider\" data-id=\"11fd063\" data-element_type=\"widget\" data-widget_type=\"divider.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-divider\">\n\t\t\t<span class=\"elementor-divider-separator\">\n\t\t\t\t\t\t<\/span>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-d876ece elementor-widget elementor-widget-text-editor\" data-id=\"d876ece\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<h2>Docking and Virtual Screening<\/h2><h3>Ensemble Docking Glide<\/h3><p>Here we use present a pipeline to perform ensemble docking to find the most probable binding mode of a given ligand in a given set (ensemble) of protein structures.<\/p><h3>Ligand-receptor interactions frequency<\/h3><p>To analyze the frequency of receptor-ligand interactions on a set of poses from a given cluster, we use scripts included on Schr\u00f6dinger Suit (v.2020-1) and in-house functional workflow built on Knime.<\/p><h3>Ligand-receptor interactions frequency multiple clusters<\/h3><p>To analyze the frequency of receptor-ligand interactions on a set of poses from different clusters, we use scripts included on Schr\u00f6dinger Suit (v.2020-3) to calculate the interactions on every pose and a in-house functional workflow built on Knime to get the frequency of interactions on each cluster and then sum the total.<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-6239a75 elementor-widget-divider--view-line elementor-widget elementor-widget-divider\" data-id=\"6239a75\" data-element_type=\"widget\" data-widget_type=\"divider.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-divider\">\n\t\t\t<span class=\"elementor-divider-separator\">\n\t\t\t\t\t\t<\/span>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-031dad7 elementor-widget elementor-widget-text-editor\" data-id=\"031dad7\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<h2>Molecular Dynamics simulations<\/h2><h3>Desmond<\/h3><h3>VMD<\/h3>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-4dfd305 elementor-widget-divider--view-line elementor-widget elementor-widget-divider\" data-id=\"4dfd305\" data-element_type=\"widget\" data-widget_type=\"divider.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-divider\">\n\t\t\t<span class=\"elementor-divider-separator\">\n\t\t\t\t\t\t<\/span>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-e0cf7f5 elementor-widget elementor-widget-text-editor\" data-id=\"e0cf7f5\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<h2>Molecular Modeling<\/h2>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-edad108 elementor-widget-divider--view-line elementor-widget elementor-widget-divider\" data-id=\"edad108\" data-element_type=\"widget\" data-widget_type=\"divider.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-divider\">\n\t\t\t<span class=\"elementor-divider-separator\">\n\t\t\t\t\t\t<\/span>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-51e352b elementor-widget elementor-widget-text-editor\" data-id=\"51e352b\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<ul id=\"myUL\"><li><h2>Miscellaneous<\/h2><p>\u00a0<\/p><\/li><li><h3>HOLE<\/h3><p>HOLE is a program that allows the analysis and visualisation of the pore dimensions of the holes through molecular structures of different proteins such as ion channels. Here we will use HOLE suite of programs to study pores in ion channels. Several HOLE programs have been used in the hole_over_time.tcl script to produce surface representations of pore cavities. You should have the HOLE programs in your computer prior to run this script.<\/p><\/li><li><h3>RMSD calculation<\/h3><p>The Root Mean Square Deviation (RMSD) is a common metric used to evaluate the distance between the predicted pose and the native pose, given a superposition of proteins or ligands.<\/p><\/li><\/ul>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-9ec5864 elementor-widget-divider--view-line elementor-widget elementor-widget-divider\" data-id=\"9ec5864\" data-element_type=\"widget\" data-widget_type=\"divider.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-divider\">\n\t\t\t<span class=\"elementor-divider-separator\">\n\t\t\t\t\t\t<\/span>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-c089301 elementor-widget elementor-widget-text-editor\" data-id=\"c089301\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<h2>Facilities<\/h2><p>The\u00a0<a href=\"https:\/\/cienciasbiologicasudec.cl\/\" target=\"_blank\" rel=\"noopener\">Facultad de Ciencias Biol\u00f3gicas<\/a>\u00a0at the\u00a0<a href=\"https:\/\/www.udec.cl\/pexterno\/\" target=\"_blank\" rel=\"noopener\">Universidad de Concepci\u00f3n<\/a>\u00a0is integrated by the departments of cell biology, biochemistry, ergonomics, pharmacology, physiology, physiopathology, and microbiology. Each department has different equipment and facilities that allow them to do cutting-edge research in their area of expertise.<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-f18eb55 elementor-widget-divider--view-line elementor-widget elementor-widget-divider\" data-id=\"f18eb55\" data-element_type=\"widget\" data-widget_type=\"divider.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-divider\">\n\t\t\t<span class=\"elementor-divider-separator\">\n\t\t\t\t\t\t<\/span>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-d7855bc elementor-widget elementor-widget-text-editor\" data-id=\"d7855bc\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<h2>Software<\/h2><p>Software for molecular simulation, modeling and Visualization: Schr\u00f6dinger Drug Design Suite, Modeller, AMBER, GROMACS, PyMol, VMD, KNIME, AutoDock, AutoDock vina, LigandScout, BIKI.<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-08b6545 elementor-widget-divider--view-line elementor-widget elementor-widget-divider\" data-id=\"08b6545\" data-element_type=\"widget\" data-widget_type=\"divider.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-divider\">\n\t\t\t<span class=\"elementor-divider-separator\">\n\t\t\t\t\t\t<\/span>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-05b7c7b elementor-widget elementor-widget-text-editor\" data-id=\"05b7c7b\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<h2>Hardware<\/h2><p>1 small GPU cluster (Tensor TWS-1686525-AMB: 2x Intel Xeon Silver 4110 Processor, 8 Core, 16 Threads, 2.1Ghz, 11M Cache, 85W. 12x 8GB DDR4 ECC\/REG 2666MHZ (96GB System memory). 1x 256GB 2.5 SATA III Internal Solid State Drive (SSD). 1x 8TB SATA 6Gb\/s 7200RPM 3.5&#8243; 256MB Cache Hard Drive. 3x GPU Nvidia Quadro P5000 16GB. CentOS 7)<\/p><p>Multiple workstations for visualization and data analysis (1x Intel CPU Core i7-7700 3.6GHz. 1x Toshiba Disco Duro 2TB Sata3 7200 rpm 64MB P300. 1x SSD 480GB Sata3 2.5&#8243;. 2x MSI Video Nvidia Gaming GeForce GTX1660 6GB. 2x Kingston DDR4 16GB 2400MHz HyperX FURY Black).<\/p><p>We have access to the CPU- GPU-clusters at the\u00a0<a href=\"https:\/\/cbsm.utalca.cl\/?page_id=18\" target=\"_blank\" rel=\"noopener\">Center for Bioinformatics and Molecular Simulations<\/a>\u00a0at Universidad de Talca, Chile<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<\/div>","protected":false},"excerpt":{"rendered":"<p>ResoursesPharmacoinformatics &#038; Systems Pharmacology Here you could find Tutorials, script library, gallery, FAQ, and a little bit more for pharmacoinformatics and drug design Search Buscar Computational polypharmacology Approved drugs from Drugbank DrugBank is a pharmaceutical knowledge database and a key pharmacoinformatics resource with comprehensive drug\/target\/disease information. In this notebook, we will download approved drugs information [&hellip;]<\/p>","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-20","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"http:\/\/ramirezlab.udec.cl\/es\/wp-json\/wp\/v2\/pages\/20","targetHints":{"allow":["GET"]}}],"collection":[{"href":"http:\/\/ramirezlab.udec.cl\/es\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"http:\/\/ramirezlab.udec.cl\/es\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"http:\/\/ramirezlab.udec.cl\/es\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/ramirezlab.udec.cl\/es\/wp-json\/wp\/v2\/comments?post=20"}],"version-history":[{"count":31,"href":"http:\/\/ramirezlab.udec.cl\/es\/wp-json\/wp\/v2\/pages\/20\/revisions"}],"predecessor-version":[{"id":1559,"href":"http:\/\/ramirezlab.udec.cl\/es\/wp-json\/wp\/v2\/pages\/20\/revisions\/1559"}],"wp:attachment":[{"href":"http:\/\/ramirezlab.udec.cl\/es\/wp-json\/wp\/v2\/media?parent=20"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}