is it possible to ab initio only a part of a protein?

Member Site Forums Rosetta 3 Rosetta 3 – General is it possible to ab initio only a part of a protein?

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    • #784

        I’ve built a homology model but a part of it (around 12aa)is not reliable because there is no homology template in this region. The whole protein is around 350aa. And I am wondering is it possible built a ab init model based on my initial model to complete these unreliable region?

      • #5011

          Why not just use CCD fragment-based loop modeling? It’s good with loops of that size.

        • #5016

            It’s worth a shot. The fragments should bias it towards whatever secondary structure it is supposed to be. CCD does not solve to prefer loops, it’s just that it’s used for loops, but is not really smart enough to keep secondary structures intact. Hopefully your fragments will get inserted and nearly close the “loop” and won’t get modified much by the CCD part.

            I have asked the abinitio people repeatedly to please document how to do “partial abinitio” as you request (you are not the first person to ask for it) and have never gotten a response. I’m sure it’s possible but I don’t know how. It may be as simple as playing with the movemap; if you want to try editing the C++ code directly we can try to see where the movemap is and tweak it to only allow your regions to change.

          • #5028

              well, IC. I hope the problem I encountered could be solved in the coming Workshop.

            • #5014

                well, but if it is not a loop for this region?

              • #5019

                  Thanks a lot for such kind helps.
                  I am not good at program and it would be nice for ab initio people provide user such kind of documentations. That’s strange for them to shrink their responsibilities without any reply.

                • #5021

                    It’s not strange if you think about it. This level of development in Rosetta is done by grad students and postdocs. Our incentive is to publish papers, not documentation. We do our best, but it’s always challenging to get the code authors to write documentation on top of papers and code. It doesn’t help that by the time a protocol has been published, it’s several years old already, so the person who wrote it may have graduated or at least moved on to other projects.

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