AutoDockFR (ADFR) - Docking with flexible receptor sidechains Overview The input for ADFR includes a receptor and a ligand in PDBQT format, prepared affinity maps, and a set of 3D- fill points that are potential ligand binding regions referred as ‘translational points’. Here we will give a step-by-step procedure to perform flexible receptor docking with ADFR with apo structure of cyclic dependent kinase protein 2 CDK2 (pdb:4EK3) and one of its ligands (pdb:1YKR). Step 1: Install MGLTools package from Downloads. Step 2: Download data.zip. UnZip the file into the directory where you will setup the calculations. The file contained prepared receptor (4EK3_rec.pdbqt) and ligands (reference: 1YKR_lig.pdbqt and input: 1YKR_random.pdbqt) files. The 1YKR_random.pdbqt is the randomized ligand structure provided as input during docking to avoid any bias to the initial ligand pose. Step 3: Prepare affinity maps and translational points. 1: Start AGFR. 2: Click on the button to load 4EK3_rec.pdbqt 3: Click on the button to load 1YKR_lig.pdbqt
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AutoDockFR (ADFR) - Docking with flexible receptor sidechainsadfr.scripps.edu/AutoDockFR/ADFR_tutorial.pdf · AutoDockFR (ADFR) - Docking with flexible receptor sidechains Overview
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OverviewThe input for ADFR includes a receptor and a ligand in PDBQT format, preparedaffinitymaps, anda set of3D- fill points that arepotential ligandbinding regionsreferred as ‘translational points’. Here we will give a step-by-step procedure toperformflexiblereceptordockingwithADFRwithapostructureofcyclicdependentkinaseprotein2CDK2(pdb:4EK3)andoneofitsligands(pdb:1YKR).
Step1:InstallMGLToolspackagefromDownloads.
Step2:Downloaddata.zip.
UnZip the file into the directory where you will setup the calculations. The filecontained prepared receptor (4EK3_rec.pdbqt) and ligands (reference:1YKR_lig.pdbqt and input: 1YKR_random.pdbqt) files. The 1YKR_random.pdbqt isthe randomized ligand structure provided as input during docking to avoidanybiastotheinitialligandpose.
UnlikeAutoDockorVina,theabove-specifiedcommands,willrunoneGAevolutionstartingwitharandomseedandwilloutputonesolution.ToexecutemultipleGAevolutionswithrandomseeds,werecommendrunningthecalculationonaclusterwheremultipleGAevolutionscanberunparallelonmultipleCPUs.WewillsoonprovidescripttorunmultipleGAevolutionsinyourlocalmachine.WehaveprovidedasupportscripttohelpsubmittingADFRjobsinaclusterbelow.RunningADFRonclusters-Executingmultipleserialjobs.-Logintoyourclusteraccount.-Installtheinstallerasdescribedondownloadssection.-ADFR jobscanthenbesubmittedmodifying theprovidedsubmissionscript.ThescriptcanbeusedbothonPBSaswellasSGEqueuingsystems. -- Change “$WHERE_YOU_INSTALLED” in the script to point to the path ofinstallationdirectory.
Step5:Analyzingresultsfrommultiplejobs.The bestScore.py script takes the “<$PATH_TO_SOLNS>” as an input, checks theresultdirectory,analysestheligandpdbqtoutputsfromallthejobsandprintsoutthebasenameof“<$PATH_TO_SOLNS>”,seedno.,lowestenergyscoreandthermsdwiththereferenceligand.Cmd:>pythonbestscore.py“<$PATH_TO_SOLNS>”.