Maybe it will be simple question but I cannot find solution by my own right now. All is about Schrodinger Maestro package.
I docked a ligand in the active centre of enzyme. The ligand is docked well and I have selected the correct type of binding.
I want to block (freeze/fix) part of it inside for further studies. For example it may be dipeptide with two R1 and R2 residues. I want to fix R1 position but also I want to elongate the R2 in-situ. My question is about how to create the R2 residues database and how to elongate it in-situ in the Maestro?
in docking, you may use constraints to not change the pose, and you may use ligand enumarition module (before the docking) for the derivatives of ligand
Dear Serdar Durgai,
thank you for your answer but i want two elongate the ligands in-situ. I do not want to do it manually. I have attached a small picture with my idea. The R1 and R2 and docked very well and I do not want to change them, moreover I want them to be fixed in docked positions. My enzyme has four binding pockets (but in theory it can have infinity).
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