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
Proteinchemist.com. 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.
THE SEQUENCE RELATIVIZER
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.
THE HYDROPATHY PLOTTER
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
THE TITRATION CURVE GENERATOR
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
THE AMINO ACID ANALYSIS TOOL
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.
THE BUFFER CALCULATOR
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.
THE AMMONIUM SULFATE CALCULATOR
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.
THE KINETICS HELPER
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.
THE SEQUENCE ANALYZER
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.