{"id":399,"date":"2019-08-01T14:57:31","date_gmt":"2019-08-01T14:57:31","guid":{"rendered":"https:\/\/ccsb.scripps.edu\/autodock\/?page_id=399"},"modified":"2024-11-14T23:49:15","modified_gmt":"2024-11-14T23:49:15","slug":"resources","status":"publish","type":"page","link":"https:\/\/ccsb.scripps.edu\/autodocksuite\/resources\/","title":{"rendered":"Resources"},"content":{"rendered":"<div class=\"fusion-fullwidth fullwidth-box fusion-builder-row-1 nonhundred-percent-fullwidth non-hundred-percent-height-scrolling\" style=\"--awb-border-radius-top-left:0px;--awb-border-radius-top-right:0px;--awb-border-radius-bottom-right:0px;--awb-border-radius-bottom-left:0px;--awb-flex-wrap:wrap;\" ><div class=\"fusion-builder-row fusion-row\"><div class=\"fusion-layout-column fusion_builder_column fusion-builder-column-0 fusion_builder_column_1_1 1_1 fusion-one-full fusion-column-first fusion-column-last\" style=\"--awb-bg-size:cover;\"><div class=\"fusion-column-wrapper fusion-flex-column-wrapper-legacy\"><div class=\"fusion-text fusion-text-1\"><h2><strong>Resources from the Docking Community<\/strong><\/h2>\n<p><strong>Databases<\/strong><\/p>\n<p><a href=\"http:\/\/www.rcsb.org\">Protein Data Bank<\/a> is the primary archive of biomolecular structure, including many structures of biomolecules with bound ligands.<\/p>\n<p><a href=\"http:\/\/zinc.docking.org\">Zinc<\/a> is a free database of commercially-available compounds for virtual screening and a great source of small molecule structures for AutoDock.<\/p>\n<p><a href=\"https:\/\/dtp.cancer.gov\/organization\/dscb\/obtaining\/available_plates.htm\">NCI Diversity Set<\/a> is a set of several thousand compounds that represent the broader chemical space of the larger NCI compounds library. You can click here for the <a href=\"https:\/\/ccsb.scripps.edu\/autodocksuite\/wp-content\/uploads\/sites\/31\/2019\/09\/NCI-Diversity-AutoDock-0.2.tar\">NCI-Diversity-AutoDock-0.2<\/a><\/p>\n<p><a href=\"https:\/\/www.bindingdb.org\/rwd\/bind\/index.jsp\">BindingDB<\/a> is a compilation of measured binding affinities of proteins with small drug-like compounds.<\/p>\n<p><strong>BindingMOAD<\/strong> was a curated subset of the PDB archive, containing all high-quality examples of ligand-protein complexes. The database is now obsolete. Read about its last update in this article: <a href=\"https:\/\/www.nature.com\/articles\/s41598-023-29996-w\">https:\/\/www.nature.com\/articles\/s41598-023-29996-w<\/a><\/p>\n<p><strong>Managing Protonation<\/strong><\/p>\n<p><a href=\"https:\/\/github.com\/rlabduke\/reduce\">Reduce<\/a> adds hydrogen positions to PDB files using standardized geometry with optimized orientations.<\/p>\n<p><strong>Setup and Visualization<\/strong><\/p>\n<p><a href=\"https:\/\/www.cgl.ucsf.edu\/chimera\/docs\/ContributedSoftware\/vina\/vina.html\">UCSF Chimera<\/a> includes setup tools for AutoDock Vina, and many options for visualization.<\/p>\n<p>Daniel Seeliger has an <a href=\"https:\/\/www3.mpibpc.mpg.de\/groups\/de_groot\/dseelig\/adplugin.html\">Autodock\/Vina plugin for PyMOL.<\/a><\/p>\n<\/div><div class=\"fusion-clearfix\"><\/div><\/div><\/div><\/div><\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-399","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ccsb.scripps.edu\/autodocksuite\/wp-json\/wp\/v2\/pages\/399","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ccsb.scripps.edu\/autodocksuite\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ccsb.scripps.edu\/autodocksuite\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ccsb.scripps.edu\/autodocksuite\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/ccsb.scripps.edu\/autodocksuite\/wp-json\/wp\/v2\/comments?post=399"}],"version-history":[{"count":5,"href":"https:\/\/ccsb.scripps.edu\/autodocksuite\/wp-json\/wp\/v2\/pages\/399\/revisions"}],"predecessor-version":[{"id":518,"href":"https:\/\/ccsb.scripps.edu\/autodocksuite\/wp-json\/wp\/v2\/pages\/399\/revisions\/518"}],"wp:attachment":[{"href":"https:\/\/ccsb.scripps.edu\/autodocksuite\/wp-json\/wp\/v2\/media?parent=399"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}