{"id":155,"date":"2015-02-04T14:21:40","date_gmt":"2015-02-04T19:21:40","guid":{"rendered":"https:\/\/research.cbc.osu.edu\/hadad.1\/?page_id=155"},"modified":"2017-10-09T10:24:35","modified_gmt":"2017-10-09T14:24:35","slug":"resources","status":"publish","type":"page","link":"https:\/\/research.cbc.osu.edu\/hadad.1\/resources\/","title":{"rendered":"Resources"},"content":{"rendered":"<p><a href=\"https:\/\/www.osc.edu\" target=\"_blank\"><img loading=\"lazy\" decoding=\"async\" class=\" wp-image-277 size-full aligncenter\" src=\"https:\/\/research.cbc.osu.edu\/hadad.1\/wp-content\/uploads\/2015\/02\/OSC.png\" alt=\"\" width=\"554\" height=\"85\" srcset=\"https:\/\/research.cbc.osu.edu\/hadad.1\/wp-content\/uploads\/2015\/02\/OSC.png 554w, https:\/\/research.cbc.osu.edu\/hadad.1\/wp-content\/uploads\/2015\/02\/OSC-300x46.png 300w\" sizes=\"auto, (max-width: 554px) 100vw, 554px\" \/><\/a><\/p>\n<p style=\"text-align: center;\">\u00a0<strong>We are indebted to the Ohio Supercomputer Center for the necessary software and resources for our research.<\/strong><\/p>\n<h2>Software<\/h2>\n<h3>Electronic Structure Calculations, Thermodynamics, Kinetics<\/h3>\n<ul>\n<li><a href=\"http:\/\/www.gaussian.com\/\" target=\"_blank\">Gaussian<\/a><\/li>\n<li><a href=\"http:\/\/www.turbomole.com\/\" target=\"_blank\">Turbomole<\/a><\/li>\n<li><a href=\"http:\/\/www.msg.ameslab.gov\/GAMESS\/\" target=\"_blank\">Gamess<\/a><\/li>\n<li><a href=\"http:\/\/www.molcas.org\" target=\"_blank\">MOLCAS<\/a>\u00a0(Excited state calculations)<\/li>\n<li><a href=\"http:\/\/www.vasp.at\" target=\"_blank\">VASP<\/a>\u00a0(Surface reactions, study of materials)<\/li>\n<\/ul>\n<h3>Molecular Dynamics Simulations, Monte Carlo Simulations<\/h3>\n<ul>\n<li><a href=\"http:\/\/ambermd.org\/\" target=\"_blank\">AMBER<\/a><\/li>\n<li><a href=\"http:\/\/www.charmm.org\/\" target=\"_blank\">CHARMM<\/a><\/li>\n<li><a href=\"http:\/\/www.schrodinger.com\/MacroModel\/\" target=\"_blank\">MacroModel<\/a><\/li>\n<\/ul>\n<h3>Modeling Ligand-Receptor Interactions<\/h3>\n<ul>\n<li><a href=\"http:\/\/dock.compbio.ucsf.edu\/\" target=\"_blank\">DOCK<\/a><\/li>\n<li><a href=\"http:\/\/autodock.scripps.edu\/\" target=\"_blank\">AutoDock<\/a><\/li>\n<li><a href=\"http:\/\/www.chemcomp.com\/software.htm\" target=\"_blank\">MOE<\/a><\/li>\n<\/ul>\n<h3>Visualization<\/h3>\n<ul>\n<li><a href=\"http:\/\/gaussian.com\/gv6new\/\" target=\"_blank\">GaussView<\/a><\/li>\n<li><a href=\"http:\/\/www.cmbi.ru.nl\/molden\/\" target=\"_blank\">Molden<\/a><\/li>\n<li><a href=\"http:\/\/www.cgl.ucsf.edu\/chimera\/\" target=\"_blank\">UCSF Chimera<\/a><\/li>\n<li><a href=\"http:\/\/www.ks.uiuc.edu\/Research\/vmd\/\" target=\"_blank\">VMD<\/a><\/li>\n<\/ul>\n<h3>Databases<\/h3>\n<ul>\n<li><a href=\"http:\/\/www.rcsb.org\/\" target=\"_blank\">Protein Data Bank<\/a><\/li>\n<li><a href=\"http:\/\/bioweb.ensam.inra.fr\/ESTHER\/general?what=index\" target=\"_blank\">ESTHER<\/a><\/li>\n<li><a href=\"http:\/\/www.isiknowledge.com\/\" target=\"_blank\">ISI Web of Knowledge<\/a><\/li>\n<li><a href=\"http:\/\/webbook.nist.gov\/chemistry\" target=\"_blank\">NIST Webbook of Chemistry<\/a><\/li>\n<li><a href=\"http:\/\/hbcpnetbase.com\/\" target=\"_blank\">CRC Handbook of Chemistry<\/a><\/li>\n<\/ul>\n<h3>Useful Links<\/h3>\n<ul>\n<li><a href=\"http:\/\/www.ilpi.com\/msds\/ref\/energyunits.html\" target=\"_blank\">Energy Unit Conversion<\/a><\/li>\n<li><a href=\"http:\/\/www.chemie.de\/tools\/mm.php3?formel=C12H10NO3P&amp;language=e&amp;submit=Calculate\" target=\"_blank\">Molecular Mass Calculator<\/a><\/li>\n<li><a href=\"http:\/\/nbcr-222.ucsd.edu\/pdb2pqr_2.1.1\/\" target=\"_blank\">PDB2PQR<\/a>\u00a0(Assigning protonation states to the amino acid residues in proteins)<\/li>\n<li><a href=\"http:\/\/www.bioinsilico.org\/ARCHPRED\/\" target=\"_blank\">ArchPRED Server<\/a>\u00a0(Loop closure for crystal structures)<\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u00a0We are indebted to the Ohio Supercomputer Center for the necessary software and resources for our research. Software Electronic Structure Calculations, Thermodynamics, Kinetics Gaussian Turbomole Gamess MOLCAS\u00a0(Excited state calculations) VASP\u00a0(Surface reactions, study of materials) Molecular Dynamics Simulations, Monte Carlo Simulations AMBER CHARMM MacroModel Modeling Ligand-Receptor Interactions DOCK AutoDock MOE Visualization GaussView Molden UCSF Chimera VMD &hellip; <a href=\"https:\/\/research.cbc.osu.edu\/hadad.1\/resources\/\" class=\"more-link\">Continue reading <span class=\"screen-reader-text\">Resources<\/span> <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":3,"featured_media":0,"parent":0,"menu_order":5,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-155","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/research.cbc.osu.edu\/hadad.1\/wp-json\/wp\/v2\/pages\/155","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/research.cbc.osu.edu\/hadad.1\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/research.cbc.osu.edu\/hadad.1\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/research.cbc.osu.edu\/hadad.1\/wp-json\/wp\/v2\/users\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/research.cbc.osu.edu\/hadad.1\/wp-json\/wp\/v2\/comments?post=155"}],"version-history":[{"count":14,"href":"https:\/\/research.cbc.osu.edu\/hadad.1\/wp-json\/wp\/v2\/pages\/155\/revisions"}],"predecessor-version":[{"id":368,"href":"https:\/\/research.cbc.osu.edu\/hadad.1\/wp-json\/wp\/v2\/pages\/155\/revisions\/368"}],"wp:attachment":[{"href":"https:\/\/research.cbc.osu.edu\/hadad.1\/wp-json\/wp\/v2\/media?parent=155"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}