sprosr compute the three dimensional strucutre of a protein
molecule using its amino acid sequences using the semidefinite programming-based
protein structure determination (SPROS) method of Ramandi (2011)
sprosr(
seq,
aco,
upl,
hydrogen_omission = 1,
f = c(10, 10, 10, 10, 10),
in_max_res = NULL,
in_min_res = NULL
)A table containing the amino acid sequence of the protein in CYANA .seq format
A table containing the angle constraint information in CYANA .aco format
A table containing the distance constraint information in CYANA .upl format
Should side-chain hydrogen atoms be omitted? TRUE/FALSE. Default is FALSE
Vector of length five detailing the multiplicative factors to be used. See details for more.
User overwrite of the maximum residue number.
User overwrite of the minimum residue number.
Matrix containing the three dimensional point configuration of the protein structure.
A list containing the final violations of the protein
The input files requires by sprosr follow the typical CYANA format. Each is a table with the following columns (no headers required).
Sequence File (seq) column 1: amino acid residue name column 2: residue number
Torsion Angle Restraint File (aco) column 1: residue number (corresponding to seq file) column 2: amino acid residue name column 3: angle identifier, one of PHI or PSI column 4: the lower limit of the angle specified in column 3 column 5: the upper limit of the angle specified in column 3
Distance Restraint File (upl) column 1: residue number of the first atom (corresponding to seq file) column 2: amino acid residue name of the first atom column 3: atom name of the first atom column 4: residue number of the second atom (corresponding to seq file) column 5: amino acid residue name of the second atom column 6: atom name of the second atom column 7: upper distance limit (in Angstroms)
Ramandi, Babak A., (2011). New Approaches to Protein NMR Automation. PhD Thesis. https://uwspace.uwaterloo.ca/bitstream/handle/10012/6389/Alipanahi_Ramandi_Babak.pdf;sequence=1