Protein Chemist's Protein Tool Kit

This page is a collection of tools for protein chemists. Each link will connect you to an interactive application for the analysis you wish to do. Looking for an application, but do not see it? Ask us about it. We will try and write one and post it. Just click on the title and a new window will open with the application running. Many of these programs are written in Java and require a Java enabled browser to run. All programs on this page were written by Darrick Carter and are copyright of The source code is available upon request. A problem frequently encountered is saving an image of the generated graphs. Due to security issues java applets may not save data onto a users computer making it difficult to store images. A work-around we recommend is holding down the -ALT- key and pressing the Print-screen key. This takes a screen snapshot which can be pasted into an image processing program for cropping and further use.

    With this tool your sequence will be used to calculate the pI, molecular weight, and hydrophobicity of your protein which will then be compared to other known proteins. Your protein will show up on a graph as red lines indicating the position of your protein in relation to others. Use this to determine if you have e.g. a very hydrophobic or acidic protein to guide in the selection of chromatography steps to use.
    This application will take a sequence pasted into the sequence window and create a hydropathy plot. An example of a plot generated with this tool is here. The published transmembrane domain for this protein is between amino acid 646 and 668. The peak of hydrophobicity is seen at around amino acid 660. The scores for hydrophobicity and hydrophilicity are based on the values given by Kyte and Doolittle [Kyte J and Doolittle RF Journal of Molecular Biology 157(6): 105-142, 1982.] using a seven amino acid averaging window.
    This program will take a sequence pasted into the sequence window and create a charge curve as a function of pH. This is useful in looking at the pI of the protein and estimating the amount of charges which may be useful in binding a protein to ion exchange resins. If the pH you wish to use generates an overall positive charge on the protein you may select a cation exchange resin; while if your protein is negatively charged you may use an anion exchanger.
    This tool is useful in teaching and learning the structures of amino acids. A pdb viewer applet drives the dispay of the amino acid structures in three dimensions. Clicking and dragging in this window allows the user to rotate and view the amino acids from various angles. An information button calls up a dialog window displaying the chemical structure and further information on the displayed amino acid. Selecting other amino acids from a sidebar will pull up their data into the display window. An example of this applet in action is found here.
    This is a simple calculation tool which allows for quick determination of the masses of chemicals needed to give the right concentration of buffer. Select from a list of 21 stored buffer types, or put in your own molecular weight for custom buffers. Give the desired concentration and volume needed and the program will give you the mass of buffer needed to make the buffer.
    Tired of digging for your ammonium sulfate table? Just select your starting concentraion of ammonium sulfate and your desired endpoint. Type in the volume you are working with and hit calculate. The program will show the mass of ammonium sulfate needed to create the new concentraion you desire. Saturation is calculated assuming zero degrees C.
    This tool accepts raw kinetic data in the form [Substrate] then a blank space, then velocity. After clicking the parse button the program's understanding of the data is presented. If this is acceptable, select the graph type you want, type your title and click plot. The graph is displayed.
    This is the prototype linker between sequence analysis programs. Current efforts areunderway to give the calculators a unified look which will allow for easy use of each sub-application. Multbot, as we call it, is going to be replaced in teh next version by a series of Java applets which will allow for powerful sequence analysis calculations. Multbot's current capabilities include Hydropathy Plots; Titration Curves; Protein Parameters (MW, pI, AA Comp, Extinction Coeff.); Drawing a sequence as a membrane protein; and UV Spectrum prediction.