Disulfide bridge

[eduardodinizRO]

Hello! I was wondering if Exprose takes into account disulfide bridges in its structure generation process. I happen to have a protein with 14 disulfide bridges and the structures generated by Exprose don't appear to have some of the disulfide bridges, in some cases presenting two cysteine residues supposed to be in a disulfide bridge with their S atoms 6 Angstrons apart. Is there a way to inform the program about this disulfide bridges?

Thank you for your attention

[jgreener64]

Hi, thanks for your interest in the software. The algorithm doesn't take disulphide bridges into account but you can add constraints for them manually. For example if you were to do

using ProteinEnsembles
constraints_com, constraints_one, constraints_two = interactions(
    "input_1.pdb",
    "input_1.dssp",
    "input_2.pdb",
    "input_2.dssp"
)

then the constraints objects are structs as in https://github.com/jgreener64/ProteinEnsembles.jl/blob/master/src/types.jl#L45-L51:

mutable struct Constraints
    atoms::Array{Atom,1}
    lower::Array{Float64,1} # List of lower constraints by present index
    upper::Array{Float64,1} # List of upper constraints by present index
    pres_inds::Array{Int,2} # List of index pairs of present constraints
end

So you can have a look at how the fields are laid out and push your own interactions into the arrays. Then run generateensemble as outlined in the readme.