Autodock
Title
Question
In assessment of receptor preparation for docking , Protein 1DWD has 3 chains. which residue has to be removed Please help. What is the criteria to delete the residue
AutoDock4 Receptor-Preparation-for-Docking 06-07 min 0-10 sec
Answers:
Hello Ma'am,
In case of 1DWD.pdb , when you open the pdb file on ADT interface, there are 3 chains visible, (chains L, H and I). When you go through the RCSB website and look at the crysrtallized structure information for 1DWD, chain H with 259 amino acids corresponds to Alpha-Thrombin (large sub-unit). Hence this is the one we need to keep and chain L and I can be deleted if desired. The ligand MID1(Inhibitor) is attached to chain H. On the ADT interface, expand residues for chain H and locate MID1 and proceed as demonstarted in the tutorial.
Please refer to the link given below for the detailed information, taken from RCSB PDB database.
https://www.rcsb.org/structure/1DWD
Hope this helps.
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