{"id":151,"date":"2018-03-01T01:12:57","date_gmt":"2018-03-01T01:12:57","guid":{"rendered":"http:\/\/sarafortuna.sites.units.it\/?page_id=151"},"modified":"2019-08-06T11:15:15","modified_gmt":"2019-08-06T11:15:15","slug":"downloads","status":"publish","type":"page","link":"https:\/\/sarafortuna.sites.units.it\/index.php\/downloads\/","title":{"rendered":"Downloads"},"content":{"rendered":"<table>\n<tbody>\n<tr>\n<td>\n<h3>BINDesignER<\/h3>\n<p><a href=\"https:\/\/github.com\/migsoler\/BINDesignER\">BINDesignER<\/a> is the computational protocotol we developed for the optimisation of peptides and for the <em>in-silico<\/em> maturation of antibody fragments. It is freely available at:<\/p>\n<p><a href=\"https:\/\/github.com\/migsoler\/BINDesignER\"> https:\/\/github.com\/migsoler\/BINDesignER<\/a><\/p>\n<p>to make it work, you will need to download few other codes, also freely available for academic use:<\/p>\n<ul>\n<li>GROMACS: <a href=\"http:\/\/manual.gromacs.org\/documentation\/2019.3\/download.html\">http:\/\/manual.gromacs.org\/documentation\/2019.3\/download.html<\/a><\/li>\n<li>SCWRL4: <a href=\"http:\/\/dunbrack.fccc.edu\/scwrl4\/\" rel=\"nofollow\">http:\/\/dunbrack.fccc.edu\/svcwrl4\/<\/a><\/li>\n<\/ul>\n<p>and a number of scoring functions. The choice of scoring function will depend on your system. For instance, for antibody fragments we\u00a0 used:<\/p>\n<ul>\n<li>Irad, Pie*Pisa, Bluues, Haddock, Bach6, <a href=\"http:\/\/bioinfo3d.cs.tau.ac.il\/FireDock\/download.html\">FireDock<\/a>, <a href=\"http:\/\/vina.scripps.edu\/\">AutoDock Vina<\/a><\/li>\n<\/ul>\n<p>while for peptides optimisation we simply used <a href=\"http:\/\/vina.scripps.edu\/\">AutoDock Vina<\/a>.<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p><strong>Programming Tutorials:<\/strong><\/p>\n<ul>\n<li><a href=\"http:\/\/www.cplusplus.com\/doc\/tutorial\/\" target=\"_blank\" rel=\"nofollow noopener\">C++ Language Tutorial<\/a><\/li>\n<li>HowTo <a href=\"http:\/\/monalisa.uniud.it\/?q=fortran-and-c\" rel=\"nofollow\">link FORTRAN and C++<\/a><\/li>\n<li><a href=\"http:\/\/it.html.net\/tutorials\/html\/\">HTML Tutorial<\/a> (in Italian)<\/li>\n<li><a href=\"http:\/\/it.html.net\/tutorials\/css\/\">CSS Tutorial<\/a> (in Italian)<\/li>\n<\/ul>\n<p><strong>Useful scripts<\/strong>:<\/p>\n<ul>\n<li>HowTo <a href=\"http:\/\/monalisa.uniud.it\/?q=beamer-poster-conversion-script\" rel=\"nofollow\">convert a LaTeX\/Beamer presentation into a poster<\/a><\/li>\n<\/ul>\n<p><strong>PhD\/PostDoc tips<\/strong>:<\/p>\n<ul>\n<li><a href=\"http:\/\/blogs.nature.com\/naturejobs\/2011\/01\/31\/how-to-be-a-successful-scientist\" target=\"_blank\" rel=\"nofollow noopener\">How to be a successful scientist<\/a>: ten commandments for being a successful scientist in academia<\/li>\n<li><a href=\"http:\/\/www.inscc.utah.edu\/%7Ereichler\/Guideforphds.pdf\" target=\"_blank\" rel=\"nofollow noopener\">Guide for PhD students<\/a> (and post-docs) aiming for a successful career in science<\/li>\n<li>Research is communication: <a href=\"http:\/\/research.microsoft.com\/en-us\/um\/people\/simonpj\/Papers\/giving-a-talk\/writing-a-paper-slides.pdf\" rel=\"nofollow\">How to write a GREAT research paper<\/a> (presentation), <a href=\"http:\/\/www-mech.eng.cam.ac.uk\/mmd\/ashby-paper-V6.pdf\" rel=\"nofollow\">How to write a paper<\/a> (30pages book).<\/li>\n<li><a href=\"http:\/\/www.tedpavlic.com\/post_resume_cv_latex_example.php\" target=\"_blank\" rel=\"nofollow noopener\">CV templates<\/a> in LaTeX, and <a href=\"http:\/\/codeinthehole.com\/tutorials\/thesisfile\/index.html\" target=\"_blank\" rel=\"nofollow noopener\">thesis<\/a> advices for LaTeX users \ud83d\ude42<\/li>\n<li><strong>Open positions (PhD\/PostDoc):<\/strong> <a href=\"http:\/\/www.psi-k.org\/\" target=\"_blank\" rel=\"nofollow noopener\">Psi-k<\/a> (materials), <a href=\"http:\/\/brightrecruits.com\/tiptop\/\" target=\"_blank\" rel=\"nofollow noopener\">TipTop<\/a> (physics), <a href=\"http:\/\/www.ccl.net\/chemistry\/announcements\/jobs\/index.shtml\" target=\"_blank\" rel=\"nofollow noopener\">CCL<\/a> (computational chemistry), <a href=\"http:\/\/academicpositions.it\/\" target=\"_blank\" rel=\"nofollow noopener\">http:\/\/academicpositions.it\/<\/a><\/li>\n<\/ul>\n<p><strong>Supervising tips<\/strong>:<\/p>\n<ul>\n<li><a href=\"http:\/\/old.iscbsc.org\/files\/p2p_Phil.pdf\" target=\"_blank\" rel=\"nofollow noopener\">Hiring and Supervising<\/a><\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n<p>&nbsp;<\/p>\n","protected":false},"excerpt":{"rendered":"<p>BINDesignER BINDesignER is the computational protocotol we developed for the optimisation of peptides and for the in-silico maturation of antibody fragments. It is freely available at: https:\/\/github.com\/migsoler\/BINDesignER to make it work, you will need to download few other codes, also freely available for academic use: GROMACS: http:\/\/manual.gromacs.org\/documentation\/2019.3\/download.html SCWRL4: http:\/\/dunbrack.fccc.edu\/svcwrl4\/ and a number of scoring functions. [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":5,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-151","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/sarafortuna.sites.units.it\/index.php\/wp-json\/wp\/v2\/pages\/151","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/sarafortuna.sites.units.it\/index.php\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/sarafortuna.sites.units.it\/index.php\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/sarafortuna.sites.units.it\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/sarafortuna.sites.units.it\/index.php\/wp-json\/wp\/v2\/comments?post=151"}],"version-history":[{"count":24,"href":"https:\/\/sarafortuna.sites.units.it\/index.php\/wp-json\/wp\/v2\/pages\/151\/revisions"}],"predecessor-version":[{"id":1033,"href":"https:\/\/sarafortuna.sites.units.it\/index.php\/wp-json\/wp\/v2\/pages\/151\/revisions\/1033"}],"wp:attachment":[{"href":"https:\/\/sarafortuna.sites.units.it\/index.php\/wp-json\/wp\/v2\/media?parent=151"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}