I was using autodock for covalent docking, and some of my compounds had very high estimated energies (e.g. +110 kcal/mol, etc.). Are these results true, or is there some error with the docking parameters?
For COVALENT docking these results are reasonable
but sometimes I run docking and I can as low as -15 kcal/mol, is that a negative sign or is it better for covalent compounds?
Make sure that the docking protocol is validated
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Molecular docking software/ websites?
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I have used Schrödinger (Glide) for docking
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In the peptide-HLA-TCR docking process, can we express the result of peptide-HLA docking in RMSD and for peptide-HLA to TCR docking, can results be expressed in binding affinity?
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