Modeling of flexible complexes

Interactive modelling (MASSHA, SASpy) and global minimization programs (SASREF, BUNCH, CORAL, GLOBSYMM)
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ThiagoVSeraphim
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Joined: 2019.11.07 23:26

Modeling of flexible complexes

#1 Post by ThiagoVSeraphim » 2020.02.07 00:23

Hello,

I have a flexible hetero-dimer and I was wondering what would be the best strategy to model this complex. Currently, there are structures of individual domains of both proteins in the complex.

Since EOM is not suitable for hetero-complexes (and I cannot fuse the two proteins and "pretend" that they are a single polypeptide chain to trick EOM, as suggested in another topic in this forum), I tried to use SASREF. Although SASREF is not designed for flexible systems, I ran it several times (~50 times), then classified obtained models using DAMCLUST. I ended up 5 different representative clusters. Is this strategy acceptable? Please, correct if I am wrong, but would these 5 clusters represent possible average conformations describing the flexible hetero-complex?

I will be happy to hear any comments/suggestions/previous experiences on that.

Thanks!
Thiago

ThiagoVSeraphim
Member
Posts: 3
Joined: 2019.11.07 23:26

Re: Modeling of flexible complexes

#2 Post by ThiagoVSeraphim » 2020.02.07 00:33

Correction: I used CORAL and not SASREF.

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