I have a crystal structure of my protein which is a homo-tetramer. I attached experimentally a peptide sequence to my recombinant monomer unit of which the structure is not solved. That's why, I did ab initio structure prediction of the attached peptide and joined both models using Chimera. Unfortunalety, since my protein is tetrameric, but I can just do the modelling and joining for an individual protein subunit, there are clashes and overlays of the joined models. Due to the fact that I do not know probable torsion angles of the bond, I was wondering if there is any tool to determine these angles and its probability? Or does someone know a tool which can be used to treat a whole homotetramer directly to avoid structure overlays?
How many amino acids make up the peptide? If the peptide is short and expected to be surface-exposed while attached to one of the units of the homo-tetramer, attach the peptide by hand and generate ensembles of structures (and energies) using molecular dynamics simulations.
chimera it's ok.. but for the future my suggestion is to try with modeller software because not only join molecules but perform a sort of minimization energy procedure during the process that is useful to avoid clash and other error. Hence, im in according with martin... submit your molecules to gromacs and perform a minimization procedure which useful to avoid your problems.
best
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