Open PyMol, and open the downloaded ligand.We will use PyMol for this purpose and never use online converters because they may ruin your ligand file. pdb format, therefore, we have to convert. Since we need the protein and the ligand to be in a.
#Brief my pymol tutorial download#
We can download the structure from the ZINC database also. We are using “sodium octanoate” as a ligand. Open PubChem (and search for the compound.Now we will prepare our ligand which we want to dock with the protein. Now we have prepared our protein structure to proceed further for docking. The chains are removed from the protein structure just to avoid complexity. After removing hetatoms, we will keep only one of the four chains (here, Chain A was taken) and remove the rest of the three chains and save this file as “protein.pdb”.We can also easily remove ligand by visualizing the protein in PyMol. If we will dock our ligand without removing the already complexed ligand, then we will not get the correct results. The structure we are using is a crystal structure complexed with ligand(s), therefore, to dock the desired ligand with the protein in that particular position we need to remove the bound ligand by removing hetatoms from the PDB file. If we know then we can easily go to step 2, but if we don’t know, then we have two options, either we can read the literature which is available on the same page of PDB from where we downloaded the structure, or we can visualize the protein structure in PyMol and note down the interacting sites of the protein. We are using Human Serum Albumin complexed with 3-carboxy-4-methyl-5-propyl-furanpropanoic acid (CMPF) (PDB ID: 2BXA).īefore proceeding further, we should make clear that whether we know the catalytic site of the protein or not. Download a protein crystal structure from PDB.We need the following files prepared for docking with AutoDock Vina: We want to bind SO in the same site where CMPF has already bound in HSA. We are docking a protein Human Serum Albumin (HSA) protein with a ligand Sodium Octanoate (SO), but HSA is already complexed with 3-carboxy-4-methyl-5-propyl-furanpropanoic acid (CMPF). This article will guide you to dock a protein with a ligand in a specific binding site/ pocket. This tool offers blind docking and binding in a specific pocket as well, which is sometimes more demanding when the binding site is already known. It provides many options depending on the needs of a user. AutoDock Vina is a bioinformatics tool that is used to perform in- silico docking of proteins with a ligand.
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