sprosr {edmcr}

Semidefinite Programming-based Protein Structure Determination

Description

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)

Usage

sprosr(
  seq,
  aco,
  upl,
  hydrogen_omission = 1,
  f = c(10, 10, 10, 10, 10),
  in_max_res = NULL,
  in_min_res = NULL
)

Arguments

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.

Details

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)

Value

X

Matrix containing the three dimensional point configuration of the protein structure.

report

A list containing the final violations of the protein

References

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