Member Site Forums Rosetta 3 Rosetta 3 – General Docking a protein into a symmetrical complex Reply To: Docking a protein into a symmetrical complex


    Hi smlewis,
    Thanks so much for your quick response. I’m running a blind docking of a protein (let’s call it A) to a layer of proteins (let’s call the monomer B) that tile as hexamers. As a result, in order to consider all possible binding sites, it would be necessary to run the docking of the A against a complex of 10 of B (one hexamer, the edges of two adjacent hexamers, and the interface where the three hexamers meet). This in and of itself is not extremely computationally intensive. However, when I was relaxing a large complex of B to prepare for the docking, it took several hours to generate one structure, while when I incorporated symmetry, a relaxed structure was generated within minutes.
    Because running relax with symmetry used resources so much better, I was curious if there was a way to dock A into a layer of B by inputting just A, the monomer of B and B’s symmetry information. Would this allow Rosetta to be similarly much more efficient with its computations? I’m planning to repeat this experiment with a variety of different layers and possible binding proteins in the future, and any increase in efficiency would be extremely helpful.
    I can think of one possible problem. It seems that if A binds asymmetrically to the layer of B, then requiring all moves of B in minimizing the energy to be identical will likely not represent reality. Perhaps I could do a low resolution dock with symmetry and then refine it in high resolution without symmetry? Again, I’m a complete beginner here and don’t know if this is possible or wise. Thanks for your time!