The simulation applets visualize the equilibria of the aforementioned reaction cases. (12) Screenshots of the user interfaces of each applet are shown in Figures S1–S4. The graph can also be exported as an SVG file by clicking the “Export graphic (SVG)” button, and the file can be opened in a graphics editor, for example in Inkscape, (9) CorelDRAW, (10) GIMP, (11) or Photoshop. The graph is implemented as a Scalable Vector Graphics (SVG) object which can be zoomed in indefinitely in the browser and resized by dragging the bottom-right corner. Adjusting the input triggers JavaScript code to update the output. In addition to text and links, an applet page consists of input elements, an output graph, and an output table. ![]() The internal calculations use mostly simple arithmetics cubic equations are solved using Newton’s method and the bisection method as fallback, and a least-squares fit algorithm has been written for the curve fitting. However, as long as the adjustable parameters are kept in the ranges of the slider elements, these effects are insignificant and almost unnoticeable. All numbers are stored internally as double-precision floating-point numbers which are fast but suffer from rounding errors and loss of precision in some cases. The mathematics have been worked out on paper and programmed as functions in JavaScript. The applets have been written in HTML, JavaScript, and CSS code and implemented as web pages that run in a web browser. The applets are freely available online (URL: ) and readily hackable for custom purposes if necessary.Ī set of four simulation applets have been developed for visualizing equilibrium concentrations. Also, a curve fitting tool is provided which roughly estimates the concentrations or the dissociation constants based on the experimental data. In general, the user is required to input the total concentrations of all proteins and ligands and the dissociation constants of all complexes, and the applets output the equilibrium concentrations of all protein species graphically as functions of concentration and as numerical values at a specified point. The latter one can be considered as either a ligand binding to two receptors or a binding of two ligands to a single receptor. ![]() The considered reactions include protein homodimerization, ligand binding to a receptor (or heterodimerization), and competitive ligand binding. These applets can be utilized for planning experiments, for verifying experimental results, and for visualization of the equilibria in education. Equilibria, even in simple systems, may not behave intuitively, which can cause misconceptions and mistakes. These reactions are simple equilibrium reactions, and the equilibrium constants, most often dissociation constant K D, are useful measures of affinity. George Wiger ( at California State University, Dominguez Hills.A set of simulation applets has been developed for visualizing the behavior of the association and dissociation reactions in protein studies. These problems are provided courtesy of Prof. The smaller window can be dragged out of the way, if it covers up any part of the main window. Results appear in the table on the main window. ![]() Determine the needed value, enter it in the cell and press "Check Answer". You will be asked to calculate the value of one the the species in the chemical equation, using the data given. When you press "New Question", a window with a chemical equation, a K value, and a set of concentrations will appear. This page is an exercise in using a balanced chemical equation and a K value to calculate a concentration. Calculating an Equilibrium Concentration Calculating an Equilibrium Concentration
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