Modelling with intra-chain contacts. CORAL/EOM

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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AJ33
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Modelling with intra-chain contacts. CORAL/EOM

#1 Post by AJ33 » 2020.06.10 11:11

Dear all,

I'm currently working on a dimer-composed of two domains (see schematic image). There are two dimerisation points for the core of the protein (1A/1B), which is then connected by linkers to domain 2. The CT of domain 2 then wraps back on itself to form a tight pocket of contacts with domain 1, before a final flexible 32 aa extension.

I'm trying to model flexibility of the linkers and final 32 CT extensions while maintaing the fixation of the 'pocket of contacts'.

I've been using CORAL to do this, but wondered if there was a better way to do this. Is EOM able to impost intra-chain constrains for a series of point contacts within a 10 aa region? or can EOM contacts only specify dimerisation interfaces.


- Or possibly I should be using a completely different program, so any input is appreciated!
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