Assignment6

Docking 1.Obtain a copy of Dock6 or Autodock and get it to run on your computer. 2. Chose one of the protein/ligand complexes from the list below. Download the PDB file from the PDB server. Prepare the protein and ligand for docking studies with whichever tool you chose. Prepare five additional molecules similar to the bound ligand and determine which of the six ligands (original plus five others) binds best.

1AAQ.pdb 1DIE.pdb 1LAH.pdb 1SRJ.pdb 2LGS.pdb 1ABE.pdb 1DWD.pdb 1LCP.pdb 1STP.pdb 2MCP.pdb 1ACJ.pdb 1EAP.pdb 1LDM.pdb 1T3R.pdb 2PHH.pdb 1ACM.pdb 1EED.pdb 1LIC.pdb 1TDB.pdb 2PK4.pdb 1AEC.pdb 1EPB.pdb 1LMO.pdb 1TKA.pdb 2PLV.pdb 1AHA.pdb 1ETA.pdb 1LNA.pdb 1TMN.pdb 2SIM.pdb 1APT.pdb 1ETR.pdb 1LPM.pdb 1TNI.pdb 2YHX.pdb 1ASE.pdb 1FEN.pdb 1LST.pdb 1TNL.pdb 3CLA.pdb 1ATL.pdb 1FKG.pdb 1MCR.pdb 1TPH.pdb 3CPA.pdb 1AZM.pdb 1FKI.pdb 1MDR.pdb 1TPP.pdb 3GCH.pdb 1BAF.pdb 1FRP.pdb 1MMQ.pdb 1TRK.pdb 3HVT.pdb 1BBP.pdb 1GHB.pdb 1MRG.pdb 1TUG.pdb 3PTB.pdb 1BLH.pdb 1GLP.pdb 1MRK.pdb 1TYL.pdb 3TPI.pdb 1BMA.pdb 1GLQ.pdb 1MUP.pdb 1UKZ.pdb 4CTS.pdb 1BYP.pdb 1HDC.pdb 1NCO.pdb 1ULB.pdb 4DFR.pdb 1CBS.pdb 1HDY.pdb 1NIS.pdb 1WAP.pdb 4EST.pdb <span style="font-family: 'Times New Roman',Times,serif;">1CBX.pdb 1HEF.pdb 1PDB.pdb 1XID.pdb 4FAB.pdb <span style="font-family: 'Times New Roman',Times,serif;">1CDG.pdb 1HFC.pdb 1PHA.pdb 1XIE.pdb 4PHV.pdb <span style="font-family: 'Times New Roman',Times,serif;">1CIL.pdb 1HRI.pdb 1PHD.pdb 2ADA.pdb 5P2P.pdb <span style="font-family: 'Times New Roman',Times,serif;">1COM.pdb 1HSL.pdb 1PHG.pdb 2AK3.pdb 6ABP.pdb <span style="font-family: 'Times New Roman',Times,serif;">1COY.pdb 1HYT.pdb 1POC.pdb 2CGR.pdb 6RNT.pdb <span style="font-family: 'Times New Roman',Times,serif;">1CPS.pdb 1ICN.pdb 1RDS.pdb 2CHT.pdb 6RSA.pdb <span style="font-family: 'Times New Roman',Times,serif;">1CTR.pdb 1IDA.pdb 1RNE.pdb 2CMD.pdb 7TIM.pdb <span style="font-family: 'Times New Roman',Times,serif;">1DBB.pdb 1IGJ.pdb 1ROB.pdb 2CTC.pdb 8GCH.pdb <span style="font-family: 'Times New Roman',Times,serif;">1DBJ.pdb 1IMB.pdb 1SLT.pdb 2DBL.pdb <span style="font-family: 'Times New Roman',Times,serif;">1DID.pdb 1IVE.pdb 1SNC.pdb 2GBP.pdb

You will want to look at the pdb file - make sure there is a bound ligand and not a dimer/trimer/tetramer structure – before making a selection