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 )
| seq | A table containing the amino acid sequence of the protein in CYANA .seq format |
|---|---|
| aco | A table containing the angle constraint information in CYANA .aco format |
| upl | A table containing the distance constraint information in CYANA .upl format |
| hydrogen_omission | Should side-chain hydrogen atoms be omitted? TRUE/FALSE. Default is FALSE |
| f | Vector of length five detailing the multiplicative factors to be used. See details for more. |
| in_max_res | User overwrite of the maximum residue number. |
| in_min_res | 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