dynamic_omes: OMES (Observed minus Expected Squared) function applied to rotamers in molecular dynamics simulations

Description

Calculates difference between observed and expected occurrences of each possible pair of rotamers (x, y) for i and j dihedral angles over all frames

Usage

dynamic_omes(
    dynamic_structure,
    rotamers,
    res_selection= 
      c("C","I","L","M","V","R","H","K","D","E","N","Q","F","Y","W","T","S","P")
  )

Value

returns a list of four elements which are numeric matrices containing (1) the correlation/covariation scores for each pair of rotamers (score), (2) the Z-scores for each pair of rotamers (Zscore), (3) the correlation/covariation scores for each pair of rotamers with zero values for autocorrelation (correlation within the same side chain) (score_noauto) and (4) the Z-scores calculated without autocorrelation pairs and zero values for autocorrelation pairs (Zscore_noauto).

Arguments

dynamic_structure: An object of class 'structure' that is created by the dynamic_structure function
rotamers: A character matrix that is produced by the angle2rotamer function. The matrix indicates the rotameric state of each side chain dihedral angle for each frame of the trajectory.
res_selection: List of amino acids that will be taken into account in the correlation/covariation matrix. By default, all the amino acids are taken into account except Gly and Ala, with no side chain dihedral angles.

Author

Antoine GARNIER, Lea BELLENGER, and Marie CHABBERT

Details

The OMES score for angles [i,j] has been computed with the following formula :

$${OMES(i,j)} = \frac{1}{N} \sum_{x,y}^{ }(N_{x,y}^{obs}(i,j)-N_{x,y}^{ex}(i,j))^2$$

with : $N_{x,y}^{ex}(i,j) = p_{x}(i)p_{y}(j)N$

where :

$N_{x,y}^{obs}(i,j)$ is number of times that each (x,y) rotamer pair is observed at angles i and j
$N_{x,y}^{ex}(i,j)$ is number of times that each (x,y) rotamer pair would be expected, based on the frequency of rotamer x and y at angles i and j
$N$ is the number of frames
$p_{x}(i)$ is the frequency of rotamer x at angle i
$p_{y}(j)$ is the frequency of rotamer y at angle j

References

Fodor AA and Aldrich RW. Influence of conservation on calculations of amino acid covariance in multiple sequence alignments. Proteins. 2004;56(2):211-21.

Examples

Run this code

  #Reading pdb and dcd files
  pdb <- system.file("rotamer/toy_coordinates.pdb", package= "Bios2cor")
  trj <- system.file("rotamer/toy_dynamics.dcd", package= "Bios2cor")

  #Creating dynamic_structure object
  wanted_frames <- seq(from = 5, to = 40, by = 10)
  dynamic_structure <- dynamic_structure(pdb, trj, wanted_frames)

  #Creating rotamers object using conversion_file
  conversion_file <- system.file("rotamer/dynameomics_rotamers.csv", package= "Bios2cor")
  rotamers <- angle2rotamer(dynamic_structure, conversion_file)

  #Creating correlation object for selected residues with OMES method
  wanted_residues <- c("W")
  omes_corr <- dynamic_omes(dynamic_structure, rotamers, wanted_residues)

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