{"id":1342,"date":"2026-08-10T07:48:38","date_gmt":"2026-08-10T07:48:38","guid":{"rendered":"https:\/\/nokobox.com\/index.php\/item\/dockamon-pyrx-1-0\/"},"modified":"2026-08-10T07:48:38","modified_gmt":"2026-08-10T07:48:38","slug":"dockamon-pyrx-1-0","status":"publish","type":"digital_item","link":"https:\/\/nokobox.com\/index.php\/item\/dockamon-pyrx-1-0\/","title":{"rendered":"Dockamon \u2013 PyRx 1.0"},"content":{"rendered":"<div class=\"w-post-elm post_content\">\n<p data-sourcepos=\"5:1-5:83\"><span style=\"vertical-align: inherit\">Dockamon \u2013 PyRx is a complete suite of molecular docking, virtual screening and ligand scoring software. Dockamon \u2013 PyRx is a structure-based drug design software package that consists of two integrated software programs. PyRx and Dockamon are complementary software that provide powerful tools for structure-based drug design. PyRx can be used to prepare structures and perform molecular docking using AutoDock and AutoDock Vina. Docking experiment results can be opened directly in Dockamon.<\/span><\/p>\n<p data-sourcepos=\"27:1-27:482\"><span style=\"vertical-align: inherit\">The Dacamon software is used to score the docked states of ligands using machine learning scoring functions. Machine learning scoring functions have been shown in the literature to have superior ability in activity estimation compared to classical scoring functions. For example, the RF-Score V2 scoring function implemented in Dacamon has an Rp value of 0.8 on the original set (trained on the refined set (v2020)), which is significantly superior to the Vina scoring function.<\/span><\/p>\n<h3><strong><span style=\"vertical-align: inherit\">Dockamon \u2013 PyRx software features and functions<\/span><br \/><\/strong><\/h3>\n<ul data-sourcepos=\"11:1-15:0\">\n<li data-sourcepos=\"11:1-11:91\"><span style=\"vertical-align: inherit\">Molecular docking: Performing molecular docking using AutoDock and AutoDock Vina software.<\/span><\/li>\n<li data-sourcepos=\"12:1-12:106\"><span style=\"vertical-align: inherit\">Virtual screening: Perform automatic docking on datasets, analyze and conveniently output results.<\/span><\/li>\n<li data-sourcepos=\"13:1-13:94\"><span style=\"vertical-align: inherit\">Ligand preparation: Perform energy optimization on ligands and convert them to PDBQT format.<\/span><\/li>\n<li data-sourcepos=\"14:1-15:0\"><span style=\"vertical-align: inherit\">Other features: Other useful functions, including a 3D molecular viewer and identification of similar compounds in the PubMed database.<\/span><\/li>\n<li data-sourcepos=\"18:1-18:141\"><span style=\"vertical-align: inherit\">Ligand Scoring: Score the docked states of ligands using machine learning scoring functions, including RF-Score V2 and SVM-Score.<\/span><\/li>\n<li data-sourcepos=\"19:1-19:100\"><span style=\"vertical-align: inherit\">Consensus scoring: Combining scores from more than one scoring function to achieve better predictions.<\/span><\/li>\n<li data-sourcepos=\"20:1-20:137\"><span style=\"vertical-align: inherit\">Protein-ligand interactions: 2D and 3D interactive visualization with broadcast quality of protein-ligand interactions. Customizable interaction options.<\/span><\/li>\n<li data-sourcepos=\"21:1-21:129\"><span style=\"vertical-align: inherit\">Protein and ligand preparation: Preparing protein and ligand structures for docking, scoring, or other molecular modeling tasks.<\/span><\/li>\n<li data-sourcepos=\"22:1-22:105\"><span style=\"vertical-align: inherit\">Infrastructure filtering and matching: Infrastructure search for SMARTS and SMILES patterns, numeric and text filtering of data.<\/span><\/li>\n<\/ul>\n<h3><span style=\"vertical-align: inherit\">System Requirements<\/span><strong>&nbsp;<\/strong><\/h3>\n<p dir=\"ltr\" style=\"text-align: left\"><strong><span style=\"vertical-align: inherit\">Minimum Requirements<\/span><\/strong><\/p>\n<div class=\"table-cell-div _3-column-table\">\n<p class=\"table-paragraph\" dir=\"ltr\" style=\"text-align: left\"><span style=\"vertical-align: inherit\">Internet Connection: Cable or DSL<\/span><\/p>\n<\/div>\n<div class=\"table-cell-div _3-column-table\">\n<p class=\"table-paragraph\" dir=\"ltr\" style=\"text-align: left\"><span style=\"vertical-align: inherit\">Operating System: Windows\u00ae 10 (latest Service Pack), 64-bit version<\/span><\/p>\n<div class=\"table-cell-div _3-column-table\">\n<p class=\"table-paragraph\" dir=\"ltr\" style=\"text-align: left\"><span style=\"vertical-align: inherit\">Computer Processor: CPU with SSE2 support, 2 cores<\/span><\/p>\n<div class=\"table-cell-div _3-column-table\">\n<p class=\"table-paragraph\" dir=\"ltr\" style=\"text-align: left\"><span style=\"vertical-align: inherit\">Computer Memory: 4 GB<\/span><\/p>\n<div class=\"table-cell-div _3-column-table\">\n<p class=\"table-paragraph\" dir=\"ltr\" style=\"text-align: left\"><span style=\"vertical-align: inherit\">Screen Resolution: 1024\u00d7768 pixels<\/span><\/p>\n<div class=\"table-cell-div _3-column-table sys-requirements-cell\">\n<p class=\"table-paragraph\" dir=\"ltr\" style=\"text-align: left\"><span style=\"vertical-align: inherit\">Graphics: OpenGL 3.2<\/span><\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<p dir=\"ltr\"><strong><span style=\"vertical-align: inherit\">Recommended Hardware<\/span><\/strong><\/p>\n<div class=\"table-cell-div _3-column-table\">\n<p class=\"table-paragraph\" dir=\"ltr\" style=\"text-align: left\"><span style=\"vertical-align: inherit\">Internet Connection: Broadband internet connection<\/span><\/p>\n<\/div>\n<div class=\"table-cell-div _3-column-table\">\n<p class=\"table-paragraph\" dir=\"ltr\" style=\"text-align: left\"><span style=\"vertical-align: inherit\">Operating System: Windows\u00ae 11 64-bit (latest Service Pack), 64-bit version<\/span><\/p>\n<div class=\"table-cell-div _3-column-table\">\n<p class=\"table-paragraph\" dir=\"ltr\" style=\"text-align: left\"><span style=\"vertical-align: inherit\">Computer Processor: CPU with SSE2 support, 8 cores<\/span><\/p>\n<div class=\"table-cell-div _3-column-table\">\n<p class=\"table-paragraph\" dir=\"ltr\" style=\"text-align: left\"><span style=\"vertical-align: inherit\">Computer Memory: 8 GB or more<\/span><\/p>\n<div class=\"table-cell-div _3-column-table\">\n<p class=\"table-paragraph\" dir=\"ltr\" style=\"text-align: left\"><span style=\"vertical-align: inherit\">Screen Resolution: 1920\u00d71080 pixels<\/span><\/p>\n<div class=\"table-cell-div _3-column-table sys-requirements-cell\">\n<p class=\"table-paragraph\" dir=\"ltr\" style=\"text-align: left\"><span style=\"vertical-align: inherit\">Graphics: OpenGL 4.6<\/span><\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<h3><span style=\"vertical-align: inherit\">Picture<\/span><\/h3>\n<p><img loading=\"lazy\" decoding=\"async\" class=\"aligncenter wp-image-954820 size-full\" src=\"https:\/\/downloadly.ir\/wp-content\/uploads\/2025\/01\/Dockamon-\u2013-PyRx-1.0-21.png\" alt=\"Dockamon \u2013 PyRx 1.0\" width=\"1412\" height=\"820\"><\/p>\n<h3><span style=\"vertical-align: inherit\">Download Link<\/span><\/h3>\n<p><a href=\"https:\/\/dl1.downloadly.ir\/Files\/Software\/Dockamon_PyRx_1.0_Downloadly.ir.rar?nocache=1785935581\"><span style=\"vertical-align: inherit\">Download Dockamon \u2013 PyRx 1.0<\/span><\/a><\/p>\n<h3><span style=\"vertical-align: inherit\">Size<\/span><\/h3>\n<p><span style=\"vertical-align: inherit\">572 MB<\/span><\/p>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>Dockamon \u2013 PyRx is a complete suite of molecular docking, virtual screening and ligand scoring software. Dockamon \u2013 PyRx is a structure-based drug design softwa<\/p>\n","protected":false},"author":1,"template":"","dgi_category":[208],"dgi_tag":[9657,9658,9659,9660],"class_list":["post-1342","digital_item","type-digital_item","status-publish","has-post-thumbnail","hentry","dgi_category-engineering-specialized","dgi_tag-dockamon-pyrx-1-0","dgi_tag-download-dockamon-pyrx","dgi_tag-free-dockamon-pyrx","dgi_tag-free-download-dockamon-pyrx"],"_links":{"self":[{"href":"https:\/\/nokobox.com\/index.php\/wp-json\/wp\/v2\/digital_item\/1342","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/nokobox.com\/index.php\/wp-json\/wp\/v2\/digital_item"}],"about":[{"href":"https:\/\/nokobox.com\/index.php\/wp-json\/wp\/v2\/types\/digital_item"}],"author":[{"embeddable":true,"href":"https:\/\/nokobox.com\/index.php\/wp-json\/wp\/v2\/users\/1"}],"version-history":[{"count":0,"href":"https:\/\/nokobox.com\/index.php\/wp-json\/wp\/v2\/digital_item\/1342\/revisions"}],"wp:attachment":[{"href":"https:\/\/nokobox.com\/index.php\/wp-json\/wp\/v2\/media?parent=1342"}],"wp:term":[{"taxonomy":"dgi_category","embeddable":true,"href":"https:\/\/nokobox.com\/index.php\/wp-json\/wp\/v2\/dgi_category?post=1342"},{"taxonomy":"dgi_tag","embeddable":true,"href":"https:\/\/nokobox.com\/index.php\/wp-json\/wp\/v2\/dgi_tag?post=1342"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}