{"id":10660,"date":"2023-12-12T16:07:00","date_gmt":"2023-12-12T16:07:00","guid":{"rendered":"https:\/\/www.blopig.com\/blog\/?p=10660"},"modified":"2023-12-12T16:07:02","modified_gmt":"2023-12-12T16:07:02","slug":"online-tools-for-drawing-and-visualizing-molecules","status":"publish","type":"post","link":"https:\/\/www.blopig.com\/blog\/2023\/12\/online-tools-for-drawing-and-visualizing-molecules\/","title":{"rendered":"Online tools for drawing and visualizing molecules"},"content":{"rendered":"\n<p><\/p>\n\n\n\n<p>I recently came across a nice tool for depicting multiple molecules called CDK Depict (thanks to Ruben for sending it to me), so I decided to explore what other web-based molecule visualization and drawing tools are available.<\/p>\n\n\n\n<!--more-->\n\n\n\n<p><a href=\"https:\/\/pubchem.ncbi.nlm.nih.gov\/\/edit3\/index.html\" data-type=\"link\" data-id=\"https:\/\/pubchem.ncbi.nlm.nih.gov\/\/edit3\/index.html\">PubChem Sketcher<\/a><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Very straightforward and easy-to-use tool for molecule drawing (or drawing from formats such as SMILES, SMARTS and InChI)<\/li>\n\n\n\n<li>Various export options for structures and images<\/li>\n\n\n\n<li>Lacks some of the sophisticated functionality of some of the other tools but does the job for simple tasks<\/li>\n<\/ul>\n\n\n\n<p><\/p>\n\n\n\n<p><a href=\"https:\/\/www.chemspider.com\/StructureSearch.aspx\" data-type=\"link\" data-id=\"https:\/\/www.chemspider.com\/StructureSearch.aspx\">ChemSpider<\/a><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Owned by the RSC and allows you to draw molecules and search the ChemSpider database (containing &gt;100 million structures) by searching for exact matches or performing similarity or substructure search)<\/li>\n\n\n\n<li>Can easily convert the structures from another format (e.g. name, SMILES, InChI) or load it from a structure or image file<\/li>\n<\/ul>\n\n\n\n<p><\/p>\n\n\n\n<p><a href=\"https:\/\/biomodel.uah.es\/en\/DIY\/JSME\/draw.en.htm\" data-type=\"link\" data-id=\"https:\/\/biomodel.uah.es\/en\/DIY\/JSME\/draw.en.htm\">BioModel<\/a><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Uses JSME and JSmol for visualising molecules in both 2D and 3D<\/li>\n\n\n\n<li>Has a few options for customizing the 3D rendering (e.g. ball and stick vs spheres, colour, element labels)<\/li>\n\n\n\n<li>Can perform optimization of the structure in 3D<\/li>\n<\/ul>\n\n\n\n<p><\/p>\n\n\n\n<p><a href=\"https:\/\/www.simolecule.com\/cdkdepict\/depict.html\" data-type=\"link\" data-id=\"https:\/\/www.simolecule.com\/cdkdepict\/depict.html\">CDK Depict<\/a><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>CDK Depict allows you to visualize (rather than draw) multiple molecules from SMILES strings or an sdf<\/li>\n\n\n\n<li>The interface is really easy to use and has various drawing options for modifying colour, annotation, hydrogens and whether to abbreviate groups and reagents<\/li>\n\n\n\n<li>Individual images can be easily downloaded as SVG, PNG or PDF files<\/li>\n\n\n\n<li>It can also be used to depict reactions<\/li>\n<\/ul>\n\n\n\n<p><\/p>\n\n\n\n<p><a href=\"https:\/\/molview.org\/\" data-type=\"link\" data-id=\"https:\/\/molview.org\/\">MolView<\/a><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>MolView is a really nice tool that allows you to draw and visualize molecules in both 2D and 3D<\/li>\n\n\n\n<li>Can also be used for visualizing macromolecules<\/li>\n\n\n\n<li>You can easily search for and view molecules in databases such as PubChem and the PDB<\/li>\n\n\n\n<li>The tools tab allows you to see calculated properties and spectroscopy data<\/li>\n\n\n\n<li>Many different export options exist, including mol, PDB and CIF file formats (in addition to image files)<\/li>\n\n\n\n<li>Overall a powerful tool with lots of additional functionality not listed here!<\/li>\n<\/ul>\n\n\n\n<p><\/p>\n\n\n\n<p>These are just a few examples and I am sure there are many more that I have missed off the list!<\/p>\n","protected":false},"excerpt":{"rendered":"<p>I recently came across a nice tool for depicting multiple molecules called CDK Depict (thanks to Ruben for sending it to me), so I decided to explore what other web-based molecule visualization and drawing tools are available.<\/p>\n","protected":false},"author":87,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"nf_dc_page":"","wikipediapreview_detectlinks":true,"_monsterinsights_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"ngg_post_thumbnail":0,"_jetpack_memberships_contains_paid_content":false,"footnotes":""},"categories":[351,201],"tags":[],"ppma_author":[637],"class_list":["post-10660","post","type-post","status-publish","format-standard","hentry","category-molecular-visualization","category-small-molecules"],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"authors":[{"term_id":637,"user_id":87,"is_guest":0,"slug":"steph","display_name":"Stephanie Wills","avatar_url":"https:\/\/secure.gravatar.com\/avatar\/4522454e01b0f43ce1309ba6fdda907c83b6966508817e94a9c4aae112253f01?s=96&d=mm&r=g","0":null,"1":"","2":"","3":"","4":"","5":"","6":"","7":"","8":""}],"_links":{"self":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/10660","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/users\/87"}],"replies":[{"embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/comments?post=10660"}],"version-history":[{"count":3,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/10660\/revisions"}],"predecessor-version":[{"id":10686,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/10660\/revisions\/10686"}],"wp:attachment":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/media?parent=10660"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/categories?post=10660"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/tags?post=10660"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/ppma_author?post=10660"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}