Which program should I use to model protein and DNA complex

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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Nature1
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Which program should I use to model protein and DNA complex

#1 Post by Nature1 » 2017.08.15 17:13

Dear Saxiers,
I am new bee in modeling/creating envelops for my protein/DNA complex. Here are list of the data that I have:
1. SAXS profile of protein and DNA complex
2. SAXS profile of DNA itself : the envelop of the DNA fits well with the simulated DNA helix
3. SAXS profile of Protein itself: the envelop of the protein fits well with its crystal structure
4. Simulated DNA helix in pdb format
5. Crystal structure of the protein
6. Simulated protein and DNA complex

Could you give me some suggestions of which program I should use to? Thank you very much

Rosie

SaxsMax
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Re: Which program should I use to model protein and DNA comp

#2 Post by SaxsMax » 2017.08.24 12:08

You could use Crysol to compute the fit from
"6. Simulated protein and DNA complex" to
"1. SAXS profile of protein and DNA complex"

If the resulting fit is not good Sasref can be applied
to arrange "4. Simulated DNA helix in pdb format" and
"5. Crystal structure of the protein" to fit
"1. SAXS profile of protein and DNA complex"

Optionally ab initio multiphase modelling can be done using Monsa
by simultaneous fitting of "1. SAXS profile of protein and DNA complex",
"2. SAXS profile of DNA itself" and "3. SAXS profile of Protein itself"

Nature1
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Joined: 2017.07.27 20:55

Re: Which program should I use to model protein and DNA comp

#3 Post by Nature1 » 2017.08.28 20:59

Thank you so much for you suggestion. I will try and let you know my update.

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