Hello, excuse me, how can I minimize a protein's energy for molecular docking? Do Swiss Target Prediction or Biovia Discovery Studio do this automatically, or does it have to be done manually? Thank you very much for your help. Best regards.
Don't know about Swiss.
But it can be done in Discovery Studio (the client version, not the free visualizer), using different algorithms like Smart Minimizer, Steepest descent, Conjugate gradient etc, using a separate but in-built tool.
However, if a crystal structure of a protein is used, especially with a co-crystallized ligand, we prefer not to minimize the protein; as we believe the crystal structure is reflecting the natural and most stable form of the protein.
In those cases, we only prepare the protein, not minimize.
It can be done by just clicking a single button in Biovia (if you have the paid client version).
It involves, adding hydrogens, completing the terminal residues, adding small missing residues (if any), adding proper charged/ protonation states of certain residues according to a specific pH.. All by clicking a single button.
Without biovia, it can be done using chimera and autodock tools. They are free
Thank you very much for your response, my friend. I'll learn how to create them later using one of those free programs you mentioned. Would you like to collaborate on the project? Could you send me your email address? I'd like to know your opinion on the molecular dockings I performed with Biovía Discovery Studio, which I think could be compromised because I didn't fully prepare the proteins and receptors. Best regards.
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