{"id":195,"date":"2021-09-07T22:02:47","date_gmt":"2021-09-08T05:02:47","guid":{"rendered":"http:\/\/labs.wsu.edu\/pmrg\/?page_id=195"},"modified":"2022-10-24T08:10:45","modified_gmt":"2022-10-24T15:10:45","slug":"lgsdataset","status":"publish","type":"page","link":"https:\/\/labs.wsu.edu\/pmrg\/resources\/lgsdataset\/","title":{"rendered":"lgsdataset"},"content":{"rendered":"<br \/>\n<section id=\"builder-section-1631585026621\" class=\"row single gutter pad-top\">\n<div style=\"\" class=\"column one \">\n<header>\n<h2>Lignin structure (LGS) Dataset<\/h2>\n<\/header>\n<div class=\"hline\"><\/div>\n<div class=\"hdr1\"><strong>About<\/strong><\/div>\n<div class=\"pfont\">LGS Dataset enumerates lignin chains for degree of polymerization ranging 3 to 25 following published monomer coupling feasibility rules. The dataset includes two types of lignin library with 60K polymer structures of milled wood lignin.<\/div>\n<div class=\"pfont\">\n<ul>\n<li>G type lignin structures which represent spruce MWL structures with 6.3K polymers<\/li>\n<li>SG type lignin structures which represent birch MWL structures with 53.7K polymers<\/li>\n<\/ul>\n<\/div>\n<div class=\"hdr1\"><strong>Download<\/strong><\/div>\n<div class=\"pfont\">You can download the databases using the links below. All the molecules are stored in canonized SMILES format and molecular data file (*.mol) compressed as zip archive. To see the structures in drawing format, we suggest any chemical structure viewer that can be visualized using SMILES \/ SDF files such as <a style=\"color: brown\" href=\"https:\/\/chemdrawdirect.perkinelmer.cloud\/js\/sample\/index.html\">ChemDraw online<\/a> for 2D structure and <a style=\"color: brown\" href=\"https:\/\/avogadro.cc\/\">Avogadro<\/a> for 3D visualization.<\/div>\n<div class=\"pfont divcolor\"><strong>Terms of use:<\/strong> The LGS dataset may be downloaded free from here and <a href=\"https:\/\/figshare.com\/s\/f04dbe377992bc8459d9\">figshare<\/a>. In published research involving LGS, cite the appropriate references mentioned below.<\/div>\n<div>\n<table id=\"tablepress-5\" class=\"tablepress tablepress-id-5 pfontgen\">\n<thead>\n<tr class=\"row-1\">\n\t<th class=\"column-1\">Dataset type<\/th><th class=\"column-2\">Description<\/th><th class=\"column-3\">Link<\/th><th class=\"column-4\">Size<\/th>\n<\/tr>\n<\/thead>\n<tbody class=\"row-hover\">\n<tr class=\"row-2\">\n\t<td class=\"column-1\"><b>G Type Structures<\/b><\/td><td colspan=\"3\" class=\"column-2\"><a style=\"color: red\" href=\"https:\/\/users.tricity.wsu.edu\/~s.eswaran\/lgsdataset\/tmapview_gtype.html\" rel=\"noopener\" target=\"_blank\">TMAP Visualization<\/a><\/td>\n<\/tr>\n<tr class=\"row-3\">\n\t<td class=\"column-1\">Molecular data file (*.mol)<\/td><td class=\"column-2\">Chemical structure file format, supported in most of molecular dynamics\u2019 software<\/td><td class=\"column-3\"><a href=\"https:\/\/s3.wp.wsu.edu\/uploads\/sites\/2775\/2021\/12\/GType_MOL.zip\">MOL File<\/a><\/td><td class=\"column-4\">14.2MB<\/td>\n<\/tr>\n<tr class=\"row-4\">\n\t<td class=\"column-1\">Connectivity and adjacency matrices (*.csv)<\/td><td class=\"column-2\">Matrices defining monomer connectivity<\/td><td class=\"column-3\"><a href=\"https:\/\/s3.wp.wsu.edu\/uploads\/sites\/2775\/2021\/12\/GType_Matrices.zip\">Metrices<\/a><\/td><td class=\"column-4\">3MB<\/td>\n<\/tr>\n<tr class=\"row-5\">\n\t<td class=\"column-1\">Comprehensive dataset (*.json)<\/td><td class=\"column-2\">Structural definition of all possible sequence in SMILES representation, evaluation structural features such as molecular weight, functional group count and bond proportion of simulated structures<\/td><td class=\"column-3\"><a href=\"https:\/\/s3.wp.wsu.edu\/uploads\/sites\/2775\/2021\/12\/GType_JSON_COMP.zip\">JSON File<\/a><\/td><td class=\"column-4\">216KB<\/td>\n<\/tr>\n<tr class=\"row-6\">\n\t<td class=\"column-1\"><b>S\/G Type Structures<\/b><\/td><td colspan=\"3\" class=\"column-2\"><a style=\"color: red\" href=\"https:\/\/users.tricity.wsu.edu\/~s.eswaran\/lgsdataset\/tmapview_sgtype.html\" rel=\"noopener\" target=\"_blank\">TMAP Visualization<\/a><\/td>\n<\/tr>\n<tr class=\"row-7\">\n\t<td class=\"column-1\">Molecular data file (*.mol)<\/td><td class=\"column-2\">Chemical structure file format, supported in most of molecular dynamics\u2019 software<\/td><td class=\"column-3\"><a href=\"https:\/\/s3.wp.wsu.edu\/uploads\/sites\/2775\/2021\/12\/SGType_MOL.zip\">MOL File<\/a><\/td><td class=\"column-4\">140MB<\/td>\n<\/tr>\n<tr class=\"row-8\">\n\t<td class=\"column-1\">Connectivity and adjacency matrices (*.csv)<\/td><td class=\"column-2\">Matrices defining monomer connectivity<\/td><td class=\"column-3\"><a href=\"https:\/\/s3.wp.wsu.edu\/uploads\/sites\/2775\/2021\/12\/SGTYpe_Matrices.zip\">Matrices<\/a><\/td><td class=\"column-4\">26.5MB<\/td>\n<\/tr>\n<tr class=\"row-9\">\n\t<td class=\"column-1\">Comprehensive dataset (*.json)<\/td><td class=\"column-2\">Structural definition of all possible sequence in SMILES representation, evaluation structural features such as molecular weight, functional group count and bond proportion of simulated structures<\/td><td class=\"column-3\"><a href=\"https:\/\/s3.wp.wsu.edu\/uploads\/sites\/2775\/2021\/12\/SGType_JSON_COMP.zip\">JSON File<\/a><\/td><td class=\"column-4\">2.3MB<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<!-- #tablepress-5 from cache --><\/div>\n<div class=\"hdr1\"><strong>Citation\u00a0<\/strong><\/div>\n<div class=\"pfont\">\n<p>Eswaran, S. c. d., Subramaniam, S., Sanyal, U., Rallo, R. &amp; Zhang, X. Molecular structural dataset of lignin macromolecule elucidating experimental structural compositions. <em>Scientific Data<\/em> <strong>9<\/strong>, 647, doi:10.1038\/s41597-022-01709-4 (2022)<\/p>\n<\/div><\/div>\n<\/section>\n<section id=\"builder-section-1632404914106\" class=\"row single gutter pad-top\">\n<div style=\"\" class=\"column one \">\n<header>\n<h2>Lignin Structure Generator Tool &amp; Usage<\/h2>\n<\/header>\n<p dir=\"auto\">Molecular structure simulation tool for lignin macromolecule. Lignin structure generator uses sequence-controlled structure generation approach for generating polymer chains of length 3 to 25. Workflow includes following functionalities<\/p>\n<p dir=\"auto\"><img decoding=\"async\" loading=\"lazy\" class=\"wp-image-446 alignright\" src=\"https:\/\/s3.wp.wsu.edu\/uploads\/sites\/2775\/2021\/11\/LGSTool-1.png\" alt=\"\" width=\"452\" height=\"281\" srcset=\"https:\/\/wpcdn.web.wsu.edu\/wp-labs\/uploads\/sites\/2775\/2021\/11\/LGSTool-1.png 718w, https:\/\/wpcdn.web.wsu.edu\/wp-labs\/uploads\/sites\/2775\/2021\/11\/LGSTool-1-396x246.png 396w\" sizes=\"(max-width: 452px) 100vw, 452px\" \/>a) Sequencing of lignin monomers and conditional linkage generation<br \/>\nb) Generating the topological matrices and directed graph representation<br \/>\nc) Converting the directed graphs into molecular structures<br \/>\nd) Validation the dataset against the experimental observations and simulated structures from previous studies<br \/>\ne) Storing the valid structures forming a dataset<\/p>\n<div>The installation and use of the source code can be found from the GitHub repository (<a href=\"https:\/\/github.com\/sudhacheran\/lignin-structure-generator\">https:\/\/github.com\/sudhacheran\/lignin-structure-generator<\/a>)<\/div>\n<\/p><\/div>\n<\/section>\n<section id=\"builder-section-1632781599194\" class=\"row single gutter pad-top\">\n<div style=\"\" class=\"column one \">\n<p>For further details, please contact: <a href=\"mailto:x.zhang@wsu.edu\">x.zhang@wsu.edu<\/a><\/p>\n<\/p><\/div>\n<\/section>\n","protected":false},"excerpt":{"rendered":"<p> <\/p>\n<h2>Lignin structure (LGS) Dataset<\/h2>\n<p><strong>About<\/strong><br \/> LGS Dataset enumerates lignin chains for degree of polymerization ranging 3 to 25 following published monomer coupling feasibility rules. The dataset includes two types of lignin library with 60K polymer structures of milled wood lignin.<\/p>\n<p>G type lignin structures which represent spruce MWL structures with 6.3K polymers<br \/> SG type lignin structures which represent birch MWL structures with 53.7K polymers<\/p>\n<p><strong>Download<\/strong><br \/> You can download the databases using the links below. All the molecules are stored in canonized SMILES format and molecular data file (*.mol) compressed as zip archive. To see the structures in drawing format, we &#8230; <a href=\"https:\/\/labs.wsu.edu\/pmrg\/resources\/lgsdataset\/\" class=\"more-link\"><span class=\"more-default\">&raquo; More &#8230;<\/span><\/a><\/p>\n","protected":false},"author":11835,"featured_media":0,"parent":188,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"template-builder.php","meta":[],"wsuwp_university_location":[],"wsuwp_university_org":[],"_links":{"self":[{"href":"https:\/\/labs.wsu.edu\/pmrg\/wp-json\/wp\/v2\/pages\/195"}],"collection":[{"href":"https:\/\/labs.wsu.edu\/pmrg\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/labs.wsu.edu\/pmrg\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/labs.wsu.edu\/pmrg\/wp-json\/wp\/v2\/users\/11835"}],"replies":[{"embeddable":true,"href":"https:\/\/labs.wsu.edu\/pmrg\/wp-json\/wp\/v2\/comments?post=195"}],"version-history":[{"count":49,"href":"https:\/\/labs.wsu.edu\/pmrg\/wp-json\/wp\/v2\/pages\/195\/revisions"}],"predecessor-version":[{"id":535,"href":"https:\/\/labs.wsu.edu\/pmrg\/wp-json\/wp\/v2\/pages\/195\/revisions\/535"}],"up":[{"embeddable":true,"href":"https:\/\/labs.wsu.edu\/pmrg\/wp-json\/wp\/v2\/pages\/188"}],"wp:attachment":[{"href":"https:\/\/labs.wsu.edu\/pmrg\/wp-json\/wp\/v2\/media?parent=195"}],"wp:term":[{"taxonomy":"wsuwp_university_location","embeddable":true,"href":"https:\/\/labs.wsu.edu\/pmrg\/wp-json\/wp\/v2\/wsuwp_university_location?post=195"},{"taxonomy":"wsuwp_university_org","embeddable":true,"href":"https:\/\/labs.wsu.edu\/pmrg\/wp-json\/wp\/v2\/wsuwp_university_org?post=195"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}