As i am working on protein-ligand docking, i want to input the x,y,z coordinates in autodock and to do that, i need the coordinates of aminoacids present in the binding site. So, PLease help me out.
If you know which atoms/amino acids you are looking for, you can just open your pdb file in a text editor: Coordinate records (lines) start with "ATOM" (amino acids and nucleotides) or "HETATM" (other molecules).
X, Y and Z coordinates are in position 31 - 38, 39 - 46 and 47 - 54 respectively (https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html)
You have to find the amino acids in the active site from the paper that publish the 3D structure or alternatively you can mine the active site residues using PyMOL if you have the 3D structure of the protein in complex with a ligand. Depending on the docking software, you can highlight the residues and adjust the grid box to cover them. PyRx works that way.
Initially you have to do literature survey to find out that, anybody has reported the binding site information about your interested protein. If the information is not available in literature then you have to predict/find the binding site residues by visualizing the protein-ligand complex in visualization tool like Pymol, Maestro etc. and you can define the binding site residues that are comes under the 5angstrom proximity of crystal/natural/bound ligand.
If your crystal structure does not have any bound ligand then you have to predict the binding site by binformatics tools or server like active site prediction server (http://www.scfbio-iitd.res.in/dock/ActiveSite.jsp), SiteMap (Schrodinger), etc.
Thank You So Much. Kiran Lokhande Ammar Danazumi Annemarie Honegger
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