Hi, I utilized one protein and several ligands for docking and measuring the Gibbs energy with Vina, while I have doubts about estimating RMSD with Python. Is it possible to use the PDB file of ligand and protein without any docking analysis as a reference and use the best structure of docking analysis for the docking file for each ligand? Or can I reference the PDB file of protein alone and compare it with the PDB format of the docking results?
To calculate RMSD in docking studies, you can first perform an initial docking analysis and use the best binding pose as your reference structure. Then, perform a second docking analysis using the same ligand-protein pair to obtain a new result. You can compare these two docking results using a Python script. For example, you can use libraries like BioPython or MDAnalysis to superimpose the reference structure with the second docking result and calculate the RMSD value. A low RMSD indicates that the positions of the two structures are similar, demonstrating the accuracy of your docking process. This approach allows you to define a reference structure and evaluate docking results effectively.
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