Hi I'm trying to model a somewhat special case.
I have a multi domain protein: A-link1-B-link2-C, where domains A, B and C are structured and described using crystallographic data. The two linkers are (presumably) flexible, however they might be linked via a disulfide bond. Is it possible to set a distance constraint for a residue in Linker1 with respect to a residue Linker2, there by gennerating a pool that lives up to the distance constarint.
I could go through the gennerated models and remove the ones that does not live up to the distance criteria, but its somewhat tedious.
Linear (OLIGOMER), and non-linear (MIXTURE) analysis, singular value decomposition (SVDPLOT), addition of missing fragments (BUNCH, CORAL), analysis of flexible systems (EOM/RANCH & GAJOE), flexible refinement of high-resolution models (SREFLEX)
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