AutoDockFR(ADFR)-Dockingwithflexiblereceptorsidechains

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.

Step3:Prepareaffinitymapsandtranslationalpoints.

1:StartAGFR.

2:Clickonthe buttontoload4EK3_rec.pdbqt

3:Clickonthe buttontoload1YKR_lig.pdbqt

4:Clickonthe buttontomakedockingboxcovertheligandand tofocustheviewonthedockingbox

Thisparticularligandoverlapswithsidechainsofthereceptor’sapoconformation.Labelthereceptorresiduesinthedockingbox( )andzoominandrotatetoobservetheoverlapoflysine33andlysine89withtheligand.

5:Clickonthe buttontosetLYS33andLYS89asresiduesmodeledwithflexiblesidechainsduringdocking

SelectedsidechainsaredisplayedasorangeSticks&Balls.Receptorsidechainstobemadeflexiblecanalsobeselectedbytypinginthetype-inwidget.

6:Checkforthegreencheckmark.Ifnottheflexibleresiduesarenotwithinthedockingbox.

Clickingonthe buttonwilladjustthedockingbox(i.e.tocoverallflexiblereceptoratoms)Thedockingboxfullycoverslysine33andlysine89andthebuttonforflexiblesidechainsvalidityisnowgreen.

7:Clickonthe“computepockets”buttontocalculatebindingpocketsAutoSiteidentifiedasinglepocketintheboxandselectedit.Thebindingpocketfill-pointsreferredas“translationalpoints”areplaceswhereADFRplacestheligandrootatom(magentaspheremesh–clickthecircledanchoricononthelefttoshowtheligandrootatom).Thebindingpocketfill-pointsvaliditybuttonisnowgreenandthe“generatemaps…”buttonisnowenabled.

8:Clickonthe“generatemaps”buttontocalculateaffinitymapsSavethemapsas4EK3_rec.zipinthedirectorywhereyouwillsetupthecalculation.Ifforanycaseyoucannotgetthezipfile,downloadithere

Step4:ExecutingADFR.Changetothedirectorywhereyouwanttorunthecalculation.LinuxandMacOSX: -openTerminaltoexecutecommands.

-cd$DIR_FOR_RUNNING_CALCULATION

Windows(Vista): -clickontheStartbuttoninthetoolbar

-Typecmd<return> toopentheWindow’scommandprompt.-cdc:\users\<USER_NAME>\$DIR_FOR_RUNNING_CALCULATION

Linuxcommand:

Ø $WHERE_YOU_INSTALLED/MGLTools2-latest/bin/adfr1YKR_random.pdbqt-m4EK3_rec.zip-r1YKR_lig.pdbqt--jobName1YKR_1--seed-1

MacOSXcommand:

Ø /Library/MGLTools2/latest/bin/adfr1YKR_random.pdbqt-m4EK3_rec.zip-r1YKR_lig.pdbqt--jobName1YKR_1--seed-1

Windowscommand:

Ø "c:\ProgramFiles\MGLTools2-latest\adfr.bat"1YKR_random.pdbqt-m4EK3_rec.zip-r1YKR_lig.pdbqt--jobName1YKR_1--seed-1

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.

cmd: > python submitzip.py –q <PBS or SGE> -n <no.of jobs> -l<input_lig.pdbqt> -r <reference_lig.pdbqt> -m <zipFile> -o <output fileprefix>

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>”.