| 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
Description
Returns a response value for given parameters at time, t.
Usage
binding1to1(t, t0, conc, kon, koff, rmax, drift = 0, offset = 0, doffset = 0)
Arguments
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. |
Examples
time <- seq(1,2000)
curve <- binding1to1(time,1000,6e-9,1000,0.01,0.6)
plot(curve)
Generate a 2:1 Binding Curve
Description
Returns a response value for given parameters at time, t.
Usage
binding2to1(
t,
t0,
conc,
kon1,
koff1,
rmax1,
kon2,
koff2,
rmax2,
drift = 0,
offset = 0,
doffset = 0
)
Arguments
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. |
Examples
time <- seq(1,2000)
curve <- binding2to1(time,1000,900e-9,10000,0.01,0.4,2000,0.0003,0.5)
plot(curve)
Response at equilibrium
Description
Returns the response value at equilibrium from concentration, Rmax and KD.
Usage
req(conc, rmax, kd)
Arguments
conc |
Analyte concentration. |
rmax |
Maximum response. |
kd |
Equilibrium dissociation constant. |
Examples
req(6e-7,1.2,6e-7)
Time to Equilibrium
Description
Returns the time taken to reach 95% equilibrium.
Usage
tteq(conc, kon, koff, theta = 0.95)
Arguments
conc |
Analyte concentration. |
kon |
Kon binding constant. |
koff |
Koff binding constant. |
theta |
Default 0.95. |
Examples
tteq(6e-7,20000,0.01)