Publications by Dave Gosser
Binding Assays
Binding Curve David Gosser 2022-03-21 Introduction Binding Curves (or Binding Assays) are an approach to determining the equilibrium constant for the interaction of two molecules, commonly used in biochemistry1. Typically, the a small molecule (commonly called the “ligand”) attaches to a larger molecule such as a protein. If we denote the pro...
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Binding Assays
Binding Curves An Introduction to Assays David Gosser 2021-10-25 Introduction Binding Curves (or Binding Assays) are an approach to determining the equilibrium constant for the interaction of two molecules, commonly used in biochemistry11 See Pollard, Thomas (2017). A Guide to Simple and Informative Binding Assays. Molecular Biology of the Cell 2...
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Systemic Treatment of Eqilibrium
this sets global command to show code chunks Systemaic Treatment of Equilibrium In solving chemical equilibrium, we often make approximation to simplify the mathematical solution. For instance, the approximation of negligible dissociation of weak acids. Here, we will explore the use of R to solve equilibrium without approximations. We find the e...
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Beer's Law and R
Beer’s Law Beer’s law for UV-Vis Spectroscopy is: \[\large Abs = \epsilon_\lambda b c \] where A = absorbance \(\epsilon_\lambda\) = absorption coefficient at a particular wavelength b = pathlength (typically cm) c = concentration (usually in molarity or \(\mu\)grams) There is a linear relationship between the abosorbance and the concentrat...
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R for Chemistry
The R Programming Language Every programming language has similar elements. We need to input data, identify variables, perform calculations, create functions, control program flow, and output data and graphics. The R language is attractive in that it has it has a full online development environment -RStudio Cloud- and built in functions for regre...
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Document
# Nonlinear Regression / Binding Curve # simulate noisy data for myoglobin KD = 0.26 [L] in kPa # includes example of a loop # data generated with random noise added # Start KD <- 0.26 # initializing variables L <- 0.0 y <- 0.0 for (i in 1:15) { y[i] <- (0.10*i/(KD+0.10*i)) + rnorm(1, sd = 0.03) ...
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sample
Beer’s Law Beer’s law for UV-Vis Spectroscopy is: \[\large Abs = \epsilon_\lambda b c \] where A = absorbance \(\epsilon_\lambda\) = absorption coefficient at a particular wavelength b = pathlength (typically cm) c = concentration (usually in molarity or \(\mu\)grams) There is a linear relationship between the abosorbance and the concentra...
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Document test
Binding Curves David Gosser 2022-01-22 Introduction Binding Curves (or Binding Assays) are an approach to determining the equilibrium constant for the interaction of two molecules, commonly used in biochemistry11 See Pollard, Thomas (2017). A Guide to Simple and Informative Binding Assays. Molecular Biology of the Cell 21(23). Typically, the a sm...
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Document
For the Binding Assay, with P = Initial Protein and L = Initial Ligand, and PL = x = amount of bound protein, we have the equilibrium expression: \(K_d = \frac{([P]-x)([L]-x)}{x}\) if we solve for x and divide by L, we will get fraction bound. \(K_d = \frac{[P][L] -[P]x -x[L] + x^2}{x}\) \(K_dx = [P][L] -[P]x -x[L] + x^2\) \([P][L] -[P]x -x[L] -K...
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R for Quantitative Chemistry
The R Programming Language Every programming language has similar elements. We need to input data, identify variables, perform calculations, create functions, control program flow, and output data and graphics. The R language is attractive in that it has it has a full online development environment -RStudio Cloud- and built in functions for regre...
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