{"id":45,"date":"2017-03-16T14:59:14","date_gmt":"2017-03-16T18:59:14","guid":{"rendered":"https:\/\/1408.mse.ncsu.edu\/yingling\/?page_id=45"},"modified":"2026-07-21T15:27:42","modified_gmt":"2026-07-21T19:27:42","slug":"software","status":"publish","type":"page","link":"https:\/\/mse.ncsu.edu\/yingling\/software\/","title":{"rendered":"Products"},"content":{"rendered":"\n\n\n\n<div class=\"has-custombg-one-background-color wp-block-ncst-button-spotlight\">\n    <div class=\"button-spotlight__container\">\n          <div class=\"button-spotlight__icon-container ncst-icon\">\n                <svg xmlns=\"http:\/\/www.w3.org\/2000\/svg\" viewBox=\"0 0 24 24\" fill=\"none\"><path d=\"M6.18422 0V1.99031H4.19391V3.98438H2.20312V24H17.8158V22.0083H19.8075V20.018H21.7969V0H6.18422ZM16.8548 23.0391H3.16266V4.94531H4.19391V22.0083H16.8548V23.0391ZM18.8466 21.0469H5.15625V2.95312H6.1875V20.018H18.8466V21.0469ZM20.8373 19.0566H7.14516V0.960938H20.8373V19.0566Z\" fill=\"currentColor\" \/><path d=\"M18.9554 3.04172H8.90723V3.80344H18.9554V3.04172Z\" fill=\"currentColor\" \/><path d=\"M18.9554 7.48593H8.90723V8.24765H18.9554V7.48593Z\" fill=\"currentColor\" \/><path d=\"M18.9554 5.24391H8.90723V6.00563H18.9554V5.24391Z\" fill=\"currentColor\" \/><path d=\"M18.9554 9.68813H8.90723V10.4498H18.9554V9.68813Z\" fill=\"currentColor\" \/><path d=\"M18.9554 11.9297H8.90723V12.6914H18.9554V11.9297Z\" fill=\"currentColor\" \/><path d=\"M18.9554 14.1319H8.90723V14.8936H18.9554V14.1319Z\" fill=\"currentColor\" \/><path d=\"M13.9913 16.3744H8.90674V17.1352H13.9913V16.3744Z\" fill=\"currentColor\" \/><\/svg>\n\n      <\/div>\n        <div class='button-spotlight__content-container'>\n      <h2 class=\"button-spotlight__heading\">Yingling Group GitHub Repository<\/h2>\n              <p class=\"button-spotlight__support\"><em>Code is deposited in the public Yingling Group <\/em><strong><em>GitHub<\/em><\/strong> <em>repository<\/em><\/p>\n            \n<div class=\"is-style-secondary wp-block-ncst-button\">\n      <a\n        class=\"ncst-block__button-link btn\"\n        href=\"https:\/\/github.com\/yingling-group\"\n        data-ncst-lightbox=\"false\"\n         target=\"_blank\"          rel=\"noreferrer noopener\"       >\n                  <span class=\"text\">Yingling Group GitHub<\/span><span class=\"arrow-indicator\"><svg class=\"wolficon wolficon-arrow-right-bold\" role=\"img\"  aria-hidden=\"true\">\n\t\t\t\n\t\t\t<use xlink:href=\"#wolficon-arrow-right-bold\">\n\t\t<\/svg><\/span>\n              <\/a>\n    <\/div>\n  \n\n    <\/div>\n  <\/div>\n<\/div>\n\n\n\n<h2 class=\"wp-block-heading\"><strong>Software (Machine Learning, Analysis and Methods)<\/strong><\/h2>\n\n\n\n<ul class=\"wp-block-list is-style-padded-list\">\n<li><a href=\"https:\/\/github.com\/yingling-group\/flory_fox_scraper\">flory_fox_scraper<\/a> Program to (a) scrape information on glass transition temperatures of polymers and (b) perform a Flory-Fox fit.\n<ul class=\"wp-block-list\">\n<li><em>Reference<\/em>: J. S. Peerless, N. J. B. Milliken, M. D. Manning, T. J. Oweida, Y. G. Yingling, Advanced Theory and Simulations (2018) <a href=\"https:\/\/doi.org\/10.1002\/adts.201800129\">DOI: 10.1002\/adts.201800129<\/a><\/li>\n<\/ul>\n<\/li>\n\n\n\n<li><a href=\"https:\/\/github.com\/yingling-group\/lammps-mspin\">lammps-mspin<\/a> LAMMPS plugin for magnetic nanoparticles simulation with atomistic resolution\n<ul class=\"wp-block-list\">\n<li><em>Reference<\/em>: Akhlak U. Mahmood and Yaroslava G. Yingling, ACS Journal of Chemical Theory and Computations (2022)<a href=\"https:\/\/pubs.acs.org\/doi\/10.1021\/acs.jctc.1c01253\"> DOI: 10.1021\/acs.jctc.1c01253<\/a><\/li>\n<\/ul>\n<\/li>\n\n\n\n<li><a href=\"http:\/\/proceedings.spiedigitallibrary.org.prox.lib.ncsu.edu\/data\/Conferences\/SPIEP\/72469\/86540W.pdf\">X3DBio2: A Visual Analysis Tool for Biomolecular Structure Comparison<br><\/a>H. Yi, S. Thakur, L. Sethaphong, Y. G. Yingling<br><strong><em>Proc. SPIE<\/em><\/strong> 8654, VDA (2013) 86540W doi:10.1117\/12.2002626<\/li>\n\n\n\n<li><a href=\"http:\/\/scitation.aip.org.prox.lib.ncsu.edu\/getpdf\/servlet\/GetPDFServlet?filetype=pdf&amp;id=PSISDG00829400000182940S000001&amp;idtype=cvips&amp;doi=10.1117\/12.906893&amp;prog=normal\">X3DBio: A Visual Analysis Tool for Biomolecular Structure Exploration<br><\/a>H. Yi, A. Singh, Y. G. Yingling. <strong><em>Proc. SPIE <\/em><\/strong>8294 (2012) 82940S-1-8<\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\">Methods<\/h2>\n\n\n\n<ul class=\"wp-block-list is-style-padded-list\">\n<li><a href=\"https:\/\/pubs.acs.org\/doi\/full\/10.1021\/acs.jctc.1c01253\">All-Atom Simulation Method for Zeeman Alignment and Dipolar Assembly of Magnetic Nanoparticles<\/a>. Akhlak U. Mahmood and Yaroslava G. Yingling. <strong><em>ACS Journal of Chemical Theory and Computations <\/em><\/strong>(2022) <a href=\"https:\/\/pubs.acs.org\/doi\/full\/10.1021\/acs.jctc.1c01253\">DOI: 10.1021\/acs.jctc.1c01253<\/a><\/li>\n\n\n\n<li><a href=\"http:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/mats.201400043\/abstract\">An Implicit Solvent Ionic Strength (ISIS) Method to Model Polyelectrolyte Systems with Dissipative Particle Dynamics<\/a>. N. K. Li, W. H. Fuss, Y. G. Yingling. <strong><em>Macromolecular Theory and Simulations <\/em><\/strong>24 (2015) 7-12.<\/li>\n\n\n\n<li><a href=\"http:\/\/pubs.acs.org\/cgi-bin\/article.cgi\/jpcbfk\/2005\/109\/i34\/pdf\/jp0527711.pdf\">Coarse-Grained Model of the Interaction of Light with Polymeric Material: Onset of Ablation<\/a>. Y. G. Yingling, B. J. Garrison. <strong><em>Journal of Physical Chemistry B<\/em><\/strong> 109 (2005) 16482-16489<\/li>\n\n\n\n<li><a href=\"http:\/\/pubs.acs.org\/cgi-bin\/article.cgi\/jpcbfk\/2004\/108\/i06\/pdf\/jp035730i.pdf\">Coarse Grained Chemical Reaction Model. <\/a>Y. G. Yingling and B. J. Garrison. <strong><em>J. Phys. Chem. B<\/em><\/strong> 108 (2004) 1815<\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\"><strong>Predicted 3D structures<\/strong><\/h2>\n\n\n<div class=\"ncst-fancy-paragraph-fifty is-text wp-block-ncst-fancy-paragraph\">\n      \n<div class=\"wp-block-ncst-fp-accompaniment\">\n    \n<div class=\"wp-block-ncst-fp-image\">\n  <figure class=\"fancy-paragraph__image-container fancy-paragraph__image-square\">\n          <a href=\"https:\/\/link.springer.com\/article\/10.1007\/s10570-020-03194-7\">\n          <img loading=\"lazy\" width=\"1023\" height=\"818\" \n        decoding=\"async\"\n        class=\"fp-image wp-image-542\"\n        src=\"https:\/\/mse.ncsu.edu\/yingling\/wp-content\/uploads\/sites\/13\/2020\/04\/90_Singh_Cellulose2020J.gif\"\n         alt=\"grid of visualizations of cellulose synthase\"               >\n          <\/a>\n          <\/figure>\n<\/div>\n\n\n  <\/div>\n\n\n<div class=\"text-only wp-block-ncst-fp-accompaniment\">\n    \n\n<h3 class=\"wp-block-heading\">Full-length cotton cellulose synthase protein (GhCESA1)<\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">In silico structure prediction of full-length cotton cellulose synthase protein (GhCESA1) and its hierarchical complexes, Abhishek Singh, Albert L. Kwansa, Ho Shin Kim, Justin T. Williams, Hui Yang, Nan K. Li, James D. Kubicki, Alison W. Roberts, Candace H. Haigler, Yaroslava G. Yingling<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong><em>Cellulose <\/em><\/strong>27 (2020) 5597-5616 <a href=\"https:\/\/link.springer.com\/article\/10.1007\/s10570-020-03194-7\">DOI: 10.1007\/s10570-020-03194-7<\/a><\/p>\n\n\n  <\/div>\n\n\n    <\/div>\n  \n\n\n<div class=\"ncst-fancy-paragraph-fifty is-text wp-block-ncst-fancy-paragraph\">\n      \n<div class=\"wp-block-ncst-fp-accompaniment\">\n    \n<div class=\"wp-block-ncst-fp-image\">\n  <figure class=\"fancy-paragraph__image-container fancy-paragraph__image-square\">\n          <a href=\"http:\/\/link.springer.com\/article\/10.1007\/s10570-015-0789-6\">\n          <img loading=\"lazy\" width=\"288\" height=\"240\" \n        decoding=\"async\"\n        class=\"fp-image wp-image-527\"\n        src=\"https:\/\/mse.ncsu.edu\/yingling\/wp-content\/uploads\/sites\/13\/2020\/01\/52_Cellulose_2015.jpg\"\n         alt=\"grid of colorful plant cellulose synthases\"          style=\"object-position:53% 81%\"       >\n          <\/a>\n          <\/figure>\n<\/div>\n\n\n  <\/div>\n\n\n<div class=\"text-only wp-block-ncst-fp-accompaniment\">\n    \n\n<h3 class=\"wp-block-heading\">Plant-specific regions of plant cellulose synthases<\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">Prediction of the structures of the plant-specific regions of vascular plant cellulose synthases and correlated functional analysis, Latsavongsakda Sethaphong, Jonathan K. Davis, Erin Slabaugh, Abhishek Singh, Candace H. Haigler, Yaroslava G. Yingling<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong><em>Cellulose<\/em><\/strong> 23 (2016) 145-161 <a href=\"https:\/\/doi.org\/10.1007\/s10570-015-0789-6\">DOI: 10.1007\/s10570-015-0789-6<\/a><\/p>\n\n\n  <\/div>\n\n\n    <\/div>\n  \n\n\n<div class=\"ncst-fancy-paragraph-fifty is-text wp-block-ncst-fancy-paragraph\">\n      \n<div class=\"wp-block-ncst-fp-accompaniment\">\n    \n<div class=\"wp-block-ncst-fp-image\">\n  <figure class=\"fancy-paragraph__image-container fancy-paragraph__image-square\">\n          <a href=\"https:\/\/doi.org\/10.1105\/tpc.15.00625\">\n          <img loading=\"lazy\" width=\"1000\" height=\"1000\" \n        decoding=\"async\"\n        class=\"fp-image wp-image-530\"\n        src=\"https:\/\/mse.ncsu.edu\/yingling\/wp-content\/uploads\/sites\/13\/2020\/01\/54_PlantCell2015.jpg\"\n         alt=\"visualization of Na+ dependent anion\"          style=\"object-position:46% 18%\" srcset=\"https:\/\/mse.ncsu.edu\/yingling\/wp-content\/uploads\/sites\/13\/2020\/01\/54_PlantCell2015.jpg 1000w, https:\/\/mse.ncsu.edu\/yingling\/wp-content\/uploads\/sites\/13\/2020\/01\/54_PlantCell2015-600x600.jpg 600w, https:\/\/mse.ncsu.edu\/yingling\/wp-content\/uploads\/sites\/13\/2020\/01\/54_PlantCell2015-800x800.jpg 800w, https:\/\/mse.ncsu.edu\/yingling\/wp-content\/uploads\/sites\/13\/2020\/01\/54_PlantCell2015-150x150.jpg 150w, https:\/\/mse.ncsu.edu\/yingling\/wp-content\/uploads\/sites\/13\/2020\/01\/54_PlantCell2015-768x768.jpg 768w, https:\/\/mse.ncsu.edu\/yingling\/wp-content\/uploads\/sites\/13\/2020\/01\/54_PlantCell2015-500x500.jpg 500w, https:\/\/mse.ncsu.edu\/yingling\/wp-content\/uploads\/sites\/13\/2020\/01\/54_PlantCell2015-992x992.jpg 992w, https:\/\/mse.ncsu.edu\/yingling\/wp-content\/uploads\/sites\/13\/2020\/01\/54_PlantCell2015-45x45.jpg 45w\" sizes=\"auto, (max-width: 1000px) 100vw, 1000px\" \/>\n          <\/a>\n          <\/figure>\n<\/div>\n\n\n  <\/div>\n\n\n<div class=\"text-only wp-block-ncst-fp-accompaniment\">\n    \n\n<h3 class=\"wp-block-heading\">Barley Efflux Protein<\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">Na+ Dependent Anion Transport by a Barley Efflux Protein Revealed through an Integrative Platform, Yagnesh Nagarajan, Jay Rongala, Sukanya Luang, Abhishek Singh, Nadim Shadiac, Julie Hayes, Tim Sutton, Matthew Gilliham, Stephen Tyerman, Gordon McPhee, Nicolas H. Voelcker, Hayden D. T. Mertens, Nigel Kirby, Jung-Goo Lee, Yaroslava G. Yingling, Maria Hrmova<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong><em>Plant Cell<\/em><\/strong> 28 (2016) 202-218 <a href=\"https:\/\/doi.org\/10.1105\/tpc.15.00625\">DOI: 10.1105\/tpc.15.00625<\/a><\/p>\n\n\n  <\/div>\n\n\n    <\/div>\n  \n\n\n<div class=\"ncst-fancy-paragraph-fifty is-text wp-block-ncst-fancy-paragraph\">\n      \n<div class=\"wp-block-ncst-fp-accompaniment\">\n    \n<div class=\"wp-block-ncst-fp-image\">\n  <figure class=\"fancy-paragraph__image-container fancy-paragraph__image-portrait\">\n          <a href=\"https:\/\/academic.oup.com\/plcell\/article-abstract\/27\/10\/2926\/6096511\">\n          <img loading=\"lazy\" width=\"144\" height=\"165\" \n        decoding=\"async\"\n        class=\"fp-image wp-image-690\"\n        src=\"https:\/\/mse.ncsu.edu\/yingling\/wp-content\/uploads\/sites\/13\/2020\/11\/50_PlantCell_2015.jpg\"\n         alt=\"visualization oof cellulose synthase interactive 1 protein\"          style=\"object-position:46% 18%\"       >\n          <\/a>\n          <\/figure>\n<\/div>\n\n\n  <\/div>\n\n\n<div class=\"text-only wp-block-ncst-fp-accompaniment\">\n    \n\n<h3 class=\"wp-block-heading\">Cellulose synthase interactive 1 protein<\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">Cellulose synthase interactive 1 is required for a fast recycling of cellulose synthase complexes to the plasma membrane in Arabidopsis,&nbsp; Lei Lei, Abhishek Singh, Logan Bashline, Shundai Li, Yaroslava G. Yingling, and Ying Gu<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong><em>Plant Cell<\/em><\/strong> (2015) <a href=\"https:\/\/academic.oup.com\/plcell\/article-abstract\/27\/10\/2926\/6096511\" target=\"_blank\" rel=\"noreferrer noopener\">DOI: 10.1105\/tpc.15.00442<\/a><\/p>\n\n\n  <\/div>\n\n\n    <\/div>\n  \n\n\n\n<ul class=\"wp-block-list is-style-padded-list\">\n<li><a href=\"http:\/\/www.pnas.org\/content\/110\/18\/7512.long\">Tertiary model of a plant cellulose synthase<br><\/a>L. Sethaphong, C. H. Haigler, J. D. Kubicki, J. Zimmer, D. Bonetta, S. DeBolt, Y. G. Yingling. <strong><em>Proc. Natl. Acad. Sci. USA<\/em><\/strong> 110 (2013) 7512-7517<\/li>\n\n\n\n<li><a href=\"http:\/\/rnajournal.cshlp.org\/cgi\/reprint\/rna.1227808v1?maxtoshow=&amp;HITS=10&amp;hits=10&amp;RESULTFORMAT=1&amp;author1=shapiro%2C+ba&amp;andorexacttitle=and&amp;andorexacttitleabs=and&amp;andorexactfulltext=and&amp;searchid=1&amp;FIRSTINDEX=0&amp;sortspec=relevance&amp;resourcetype=HWCIT\">The 3\u2032 Proximal Translational Enhancer of Turnip Crinkle Virus Binds to 60S Ribosomal Subunits<br><\/a>V. A. Stupina, A. Meskauskas, J. C. Mccormack, Y. G. Yingling, B. A. Shapiro, J. D. Dinman, A. E. Simon. <strong><em>RNA<\/em><\/strong> 14 (2008) 2379-2393<\/li>\n\n\n\n<li><a href=\"http:\/\/jvi.asm.org\/cgi\/reprint\/82\/17\/8706\">Structural Domains Within the 3\u2032 UTR of Turnip Crinkle Virus<br><\/a>J. C. McCormack, X. Yuan, Y. G. Yingling, W. Kasprzak, R. E. Zamora, B. A. Shapiro, A. E. Simon. <strong><em>Journal of Virology<\/em><\/strong> 82 (2008) 8706-8720<\/li>\n\n\n\n<li><a href=\"http:\/\/pubs.acs.org\/cgi-bin\/article.cgi\/nalefd\/2007\/7\/i08\/pdf\/nl070984r.pdf\">Computational design of an RNA hexagonal nano-ring and an RNA nanotube. <\/a>Y. G. Yingling, B. A. Shapiro. <strong><em>Nano Letters<\/em><\/strong> 7 (2007) 2328-2334<\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\">Database<\/h2>\n\n\n\n<p class=\"wp-block-paragraph\"><a href=\"http:\/\/nar.oxfordjournals.org\/cgi\/reprint\/gkm842v1\">RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign<br><\/a>E.Bindewald, R. Hayes, Y. G. Yingling, W. Kasprzak, B. A. Shapiro<br><strong><em>Nucleic Acids Res. <\/em><\/strong>36 (2008) D392-D397<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Link to <a href=\"http:\/\/rnajunction.abcc.ncifcrf.gov\/\">RNAJunction database<\/a><\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Patents<\/h2>\n\n\n\n<ol class=\"wp-block-list is-style-padded-list\">\n<li>K. Clendennen,\u00a0Y. G. Yingling,\u00a0H. Kim,\u00a0(2018),\u00a0CALB Variants, US010035995 B2\u00a0<a href=\"https:\/\/www.google.com\/patents\/WO2017100240A1?cl=en\">WO2017100240 A1<\/a>. The invention relates to amino acid sequence variants of a lipase with improved activity for catalyzing synthesis reactions and methods of preparing the variants. The methods include predicting amino acid sites for change based on computational models of the protein structure in non-aqueous conditions, and expressing the protein in a prokaryotic host for subsequent purification and use. The enzyme sequence variants described have a three to nine-fold improvement in synthesis activity over the parent protein sequence.<\/li>\n\n\n\n<li>A. Shapiro,\u00a0Y. G. Yingling, E. Bindewald, W. Kasprzak, L. Jaeger, I. Severcan, C. Geary, K. Afonin (2010), RNA Nanoparticles and methods of use, WO2010148085-A1,\u00a0<a href=\"https:\/\/www.google.com\/patents\/US20120263648\">US 20120263648 A1<\/a>. The presently-disclosed subject matter relates to an artificial RNA nanostructure and method of use thereof. In particular, the presently-disclosed subject matter relates to RNA nanoparticles and RNA dendrimers, and methods of disease diagnosis and treatments using the RNA nanostructure and RNA dendrimers.<\/li>\n\n\n\n<li>G. Yingling, B. A. Shapiro (2007), RNA nanoparticles and nanotubes.\u00a0<a href=\"https:\/\/patents.google.com\/patent\/EP2035043A2\/en?oq=EP2035043-A2\">EP2035043-A2<\/a>; AU2007300734-A1; CA2654174-A1; US2010016409-A1. The instant invention provides polyvalent RNA nanoparticles comprising RNA motifs as building blocks that can form RNA nanotubes. The polyvalent RNA nanoparticles are suitable for therapeutic or diagnostic use in a number of diseases or disorders.<\/li>\n<\/ol>\n","protected":false},"excerpt":{"rendered":"<p>Software (Machine Learning, Analysis and Methods) Methods Predicted 3D structures Database RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesignE.Bindewald, R. Hayes, Y. G. Yingling, W. Kasprzak, B. A. ShapiroNucleic Acids Res. 36 (2008) D392-D397 Link to RNAJunction database Patents<\/p>\n","protected":false},"author":12,"featured_media":0,"parent":0,"menu_order":11,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"source":"","ncst_custom_author":"","ncst_show_custom_author":false,"ncst_dynamicHeaderBlockName":"ncst\/default-header","ncst_dynamicHeaderData":"{}","ncst_content_audit_freq":"","ncst_content_audit_date":"","ncst_content_audit_display":false,"ncst_backToTopFlag":"","footnotes":""},"class_list":["post-45","page","type-page","status-publish","hentry"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.9 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Products - Yingling Research Group<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/mse.ncsu.edu\/yingling\/software\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Products - Yingling Research Group\" \/>\n<meta property=\"og:description\" content=\"Software (Machine Learning, Analysis and Methods) Methods Predicted 3D structures Database RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesignE.Bindewald, R. Hayes, Y. G. Yingling, W. Kasprzak, B. A. 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Hayes, Y. G. Yingling, W. Kasprzak, B. A. 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