Is there a package that can compute the molecular mass based on an amino acid sequence?
MolecularGraph has the machinery, but that appears to be focused on small molecules.
I can’t find a method in BioSequences
Probably not what you want, but from the PDB file you can do this:
julia> using PDBTools
julia> pdb = wget("1LBD")
Array{Atoms,1} with 1870 atoms with fields:
index name resname chain resnum residue x y z beta occup model segname index_pdb
1 N SER A 225 1 45.228 84.358 70.638 67.05 1.00 1 - 1
2 CA SER A 225 1 46.080 83.165 70.327 68.73 1.00 1 - 2
3 C SER A 225 1 45.257 81.872 70.236 67.90 1.00 1 - 3
⋮
1868 OG1 THR A 462 238 -27.462 74.325 48.885 79.98 1.00 1 - 1868
1869 CG2 THR A 462 238 -27.063 71.965 49.222 78.62 1.00 1 - 1869
1870 OXT THR A 462 238 -25.379 71.816 51.613 84.35 1.00 1 - 1870
julia> mass(pdb)
24719.768399999957
julia> formula(pdb)
C₁₁₉₂N₃₂₀O₃₄₆S₁₂
1 Like
Thanks for the link. I was not aware of PDBTools. I looked in BioStructures.jl, but did not find anything,
I love the formula 
I don’t normally have a PDB-file, but now we have alphafold, so maybe 
It’s not in BioStructures.jl - PRs welcome of course.
Well, that was really easy (not surprisingly) to implement in PDBTools. Now you can do (with version 0.12.12, which will be available at any moment):
julia> using PDBTools
julia> seq = "ATVR"
"ATVR"
julia> mass(Sequence(seq))
427.4986
julia> seq = ["ARG", "THR", "GLU"]
3-element Vector{String}:
"ARG"
"THR"
"GLU"
julia> mass(Sequence(seq))
386.4036
It does not handle terminals in any sense, it is just the sum of the average mass (isopically speaking) of the amino acid residues in the sequence.
1 Like
Thank you so much @lmiq . This is exactly what I need!
How I just love this community!
1 Like