Description Usage Arguments Details Value References
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)
1 2 3 4 5 6 7 8 9 |
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. |
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)
X |
Matrix containing the three dimensional point configuration of the protein structure. |
report |
A list containing the final violations of the protein |
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
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