I am trying to do both docking and molecular dynamics simulation. Should I minimise the protein structure after adding amino acids far from active site before docking? I have taken a PDB structure with co crystallized ligand.
If you take/ modify/ replace amino acid from protein sequence you should minimize the structure before docking.. It has been seen that the remote modifications may influence the active site structure and therefore ligand bonding.
If you take/ modify/ replace amino acid from protein sequence you should minimize the structure before docking.. It has been seen that the remote modifications may influence the active site structure and therefore ligand bonding.
Yes, it is advisable to minimize the protein structure as there are relatively good chances that any modification you make may lead to changes in the intra-protein networks and may affect the confidence of the subsequent docking results.
Sudarshan Lamichhane... I agree with Nayim Sepay Unless you make modifications in the protein crystal structure (introducing mutations, removing ligand or cofactor, adding missing residues), you don't have to energy minimize the structure. However, if you find there are missing bonds or residues, you need to minimize the protein structure. This is not just for the influence in the active site but also your protein might experience steric clashes or unfavourable bonds.
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