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  • that bind to your target protein Click here to see the requirements for using this portal Click to Start Docking Create a TACC Account here Contact Stan Watowich at UTMB to request he add you to his allocation Come back here and get Docking Why all this This portal uses TACC s Lonestar supercomputer to make these docking runs take 1 hour plus queue wait time instead of a week

    Original URL path: https://drugdiscovery.tacc.utexas.edu/ (2015-04-29)
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  • Autodock Vina File Upload
    Submit Job View Jobs Manage Files Protein Upload Form Click to Select File Uploaded Files Home About Top FAQ Texas Advanced Computing Center University of Texas Medical Branch

    Original URL path: https://drugdiscovery.tacc.utexas.edu/pages/upload.html (2015-04-29)
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  • TACC Docking Portal FAQ
    from the existing docking portal run at UTMB Docking At UTMB In order to scale the size of the docking computations the portal needed to be rewritten to work with TACC s infrastructure A collaboration was launched between Dr Stan Watowich and Usha Viswanathan at UTMB and Stephen Mock and John Fonner at TACC to build the portal infrastructure and docking execution pipeline to run on TACC s high performance

    Original URL path: https://drugdiscovery.tacc.utexas.edu/pages/about.html (2015-04-29)
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  • TACC Docking Portal FAQ
    20 SAdenosylHomocysteineHydrolase 1159 33 TyrosineKinaseSRC 5793 155 Thrombin 2292 65 ThymidineKinase 784 22 Trypsin 1544 44 VascularEndothelialGrowthFactorReceptor2 2641 74 1 Benchmarking Sets for Molecular Docking 2006 N Huang B K Shoichet and John Irwin J Med Chem 49 6789 6801 2 Comparison of Several Molecular Docking Programs Pose Prediction and Virtual Screening Accuracy 2009 J B Cross D C Thompson B K Rai J C Baber K Y Fan Y Hu and C Humblet J Chem Inf Model 49 1455 1474 What parameters do I input Job Name A project name descriptor to help you remember which job this is Protein File Click the Click to Select File text and upload your protein file from your computer The uploading can take some time depending on the size of your protein and connection speed Active Site Enter an x y z to designate the center of the search volume Typically this coordinate is the center of the protein s active site Grid Size Specify in Angstroms the size of the box around the active site to search within Too large a value can lead to inaccurate binding positions outside of the active site A good start is a box 24 x 24 x 24 A Database Enter the ligand database to search against for any database results are typically returned the same day What will the DrugDiscovery TACC portal return to me Log A log file describing the tasks performed and noting any warnings or errors Report A file listing the top 500 binders sorted such that the best lowest score is first The ligands are referenced by ZINC codes and these can be extracted and pasted into the ZINC web site to return chemical structures catalog numbers etc Top Results A folder containing the top 500 binders each with their top five poses in PDB format Additionally a separate log file for each binder containing the Vina scores for it s five best poses Protein pdbqt A file containing the target protein in PDBQT format What small molecule libraries are available A ZINC Lrg library of 642 759 commercially available drug like uncharged Lipinski ROF molecules that can be screened against a target protein in 6 12 hours This library is a custom subset of the ZINC Database filtered to contain only clean drug like compounds from the vendors ChemBridge ChemDiv Ryan Scientific Maybridge and Sigma Aldrich Dr John Irwin UCSF graciously generated this very large library for us A ZINC Sm library of 46 702 molecules combines the Maybridge Hitfinder and Chembridge screening libraries that were on our original Docking UTMB portal the TACC computers can screen this library in 2 6 hours The component libraries had the following properties Maybridge compounds were filtered to have the following properties net charge 0 9 rotatable bonds 11 H bond acceptors MW 250 650 Da and clogP 1 This produced 5 000 drug like molecules that are expected to have improved solubility Chembridge compounds were filtered to have the following properties

    Original URL path: https://drugdiscovery.tacc.utexas.edu/pages/faq.html (2015-04-29)
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    Original URL path: /pages/uploadIFrame.html (2015-04-29)




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