one of the proteins I am trying to dock has a phosphorylation at one of the residues and i want to dock it , without changing that residue, which tool can be used for such non standard, post translationally modified amino acid containing protein docking?
When dealing with protein-protein docking involving non-standard amino acids, it's important to choose a computational tool that supports these non-standard residues. One such tool that can handle non-standard amino acids is HADDOCK (High Ambiguity-Driven Biomolecular DOCKing).
HADDOCK allows for flexibility in defining molecular interactions, which can be crucial when dealing with non-standard amino acids or modified residues. It supports the use of user-defined restraints, making it adaptable to various types of molecules and molecular features.
Here are the general steps you might follow with HADDOCK:
Prepare Input Files: Prepare PDB files for both interacting proteins, including the non-standard amino acids. Define any additional parameters required for the non-standard amino acids. Define Active and Passive Residues: Specify the residues that are considered active or passive in the binding site. Run HADDOCK: Submit the job to the HADDOCK server or run it locally. Analyze Results: Analyze the docking results, considering the interactions involving non-standard amino acids.
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