Help for package pbm (original) (raw)

Title:	Protein Binding Models
Version:	1.2.1
Description:	Binding models which are useful when analysing protein-ligand interactions by techniques such as Biolayer Interferometry (BLI) or Surface Plasmon Resonance (SPR). Naman B. Shah, Thomas M. Duncan (2014) <doi:10.3791/51383>. Hoang H. Nguyen et al. (2015) <doi:10.3390/s150510481>. After initial binding parameters are known, binding curves can be simulated and parameters can be varied. The models within this package may also be used to fit a curve to measured binding data using non-linear regression.
Depends:	R (≥ 3.4.4)
License:	MIT + file LICENSE
Encoding:	UTF-8
URL:	https://github.com/jonathanrd/pbm
BugReports:	https://github.com/jonathanrd/pbm/issues
RoxygenNote:	7.1.1
Suggests:	testthat, knitr, rmarkdown, ggplot2, gridExtra
VignetteBuilder:	knitr
NeedsCompilation:	no
Packaged:	2021-03-28 07:20:40 UTC; jonathan
Author:	Jonathan Davies [aut, cre]
Maintainer:	Jonathan Davies jonathanrd@gmail.com
Repository:	CRAN
Date/Publication:	2021-03-28 14:50:18 UTC

Generate a 1:1 Binding Curve

Returns a response value for given parameters at time, t.

binding1to1(t, t0, conc, kon, koff, rmax, drift = 0, offset = 0, doffset = 0)

t	Time.
t0	Time of dissociation.
conc	Analyte concentration.
kon	Kon binding constant.
koff	Koff binding constant.
rmax	Maximum response, Rmax.
drift	Optional. Parameter to add a linear baseline drift.
offset	Optional. Applies a global offset to the response value.
doffset	Optional. Applies an offset at the start of dissociation.

time <- seq(1,2000)
curve <- binding1to1(time,1000,6e-9,1000,0.01,0.6)
plot(curve)

Returns a response value for given parameters at time, t.

binding2to1(
  t,
  t0,
  conc,
  kon1,
  koff1,
  rmax1,
  kon2,
  koff2,
  rmax2,
  drift = 0,
  offset = 0,
  doffset = 0
)

t	Time.
t0	Time of dissociation.
conc	Analyte concentration.
kon1	Kon binding constant for first component.
koff1	Koff binding constant for first component.
rmax1	Maximum response, Rmax, for first component.
kon2	Kon binding constant for second component.
koff2	Koff binding constant for second component.
rmax2	Maximum response, Rmax, for second component.
drift	Optional. Parameter to add a linear baseline drift.
offset	Optional. Applies a global offset to the response value.
doffset	Optional. Applies an offset at the start of dissociation.

time <- seq(1,2000)
curve <- binding2to1(time,1000,900e-9,10000,0.01,0.4,2000,0.0003,0.5)
plot(curve)

Returns the response value at equilibrium from concentration, Rmax and KD.

req(conc, rmax, kd)

conc	Analyte concentration.
rmax	Maximum response.
kd	Equilibrium dissociation constant.

req(6e-7,1.2,6e-7)

Returns the time taken to reach 95% equilibrium.

tteq(conc, kon, koff, theta = 0.95)

tteq(6e-7,20000,0.01)