NormalizedBvalue: B-value Normalization

In vanddraabe: Identification and Statistical Analysis of Conserved Waters Near Proteins

Description

Calculate the normalized B-value values of waters for a structure.

Usage

NormalizedBvalue(Bvalues)

Arguments

Bvalues

B-value values

Details

The normalized B-value values are the number of standard deviations from the mean for the water oxygens' B-values within the structure of interest.

The B-value normalization exclusion value is user defined within the main ConservedWaters() function but has a default value of 1.0.

Value

Vector of normalized and unitless B-value values.

Author(s)

Emilio Xavier Esposito [e-mail]

References

Oliviero Carugo. Correlation between occupancy and B value of water molecules in protein crystal structures. Protein Engineering, 1999, 12 (12), pp 1021-1024. DOI: 10.1093/protein/12.12.1021 PMID: 10611392

See Also

Other "Bound Water Environment": BoundWaterEnvironment.interact, BoundWaterEnvironment.quality, BoundWaterEnvironment, Mobility, calcBvalue, calcNearbyHydrationFraction, calcNumHydrogenBonds

Examples

  set.seed(13)
  Bvalues <- sample(thrombin.1hai$atom$b, 10)
  Bvalues
  # [1] 45.73 45.40 20.24 39.30 35.53
  #     22.16 35.81 15.35 22.73 21.34
  NormalizedBvalue(Bvalues)
  # [1]  1.3698  1.3404 -0.9017  0.7968  0.4608
  #     -0.7306  0.4858 -1.3375 -0.6798 -0.8037

vanddraabe documentation built on June 8, 2019, 1:03 a.m.