Index for the sdENM ff — sdENM • Bio3D

A dictonary of spring force constants for the sdENM force field.

data(sdENM)

Format

An array of 27 matrices containg the spring force constants for the ‘sdENM’ force field (see Dehouch et al for more information). Each matrix in the array holds the force constants for all amino acid pairs for a specific distance range.

See examples for more details.

Source

Dehouck Y. & Mikhailov A.S. (2013) PLoS Comput Biol 9:e1003209.

References

Skjaerven, L. et al. (2014) BMC Bioinformatics 15, 399. Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696. Dehouck Y. et al. (2013) PLoS Comput Biol 9:e1003209.

Examples

## Load force constant data
data(sdENM)

## force constants for amino acids A, C, D, E, and F
## in distance range [4, 4.5)
sdENM[1:5, 1:5, 1]
#>       A      C     D     E     F
#> A 2.469  3.711 0.988 2.603 4.171
#> C    NA 10.227 3.320 2.923 4.599
#> D    NA     NA 3.535 2.786 3.012
#> E    NA     NA    NA 5.286 4.165
#> F    NA     NA    NA    NA 4.874

## and distance range [4.5, 5)
sdENM[1:5, 1:5, 2]
#>       A     C     D     E     F
#> A 3.282 2.792 3.875 3.220 3.105
#> C    NA 1.944 3.478 2.543 4.895
#> D    NA    NA 2.025 1.991 4.525
#> E    NA    NA    NA 4.250 3.288
#> F    NA    NA    NA    NA 3.846

## amino acid pair A-P, at distance 4.2
sdENM["A", "P", 1]
#> [1] 7.593

if (FALSE) {
## for use in NMA
pdb <- read.pdb( system.file("examples/1hel.pdb", package="bio3d") )
modes <- nma(pdb, ff="sdenm")
}