WinPep

WinPep (and Wingene) is a super handy tool designed for analyzing polypeptide sequences. If you're diving into the world of amino acids, this little app has got your back!

Amino Acid Sequence Analysis Made Easy

With WinPep, you get a bunch of options to analyze amino acid sequences. First up, it can pull basic physicochemical properties for you, like:

• Sequence length


• Amino acid occurrence frequencies


• Isoelectric point [pKa values from Creighton (3)]


• Molecular weight and molar absorption coefficients for both native and denatured proteins.

If you need something more in-depth, you can simulate sequence-specific cleavage of the protein! Just pick one of the preset proteases or chemical agents, or even enter your own recognition sequence. Then, it shows all the possible peptide fragments with their sequence position, length, and molecular weight. This makes it super easy to identify fragments after HPLC and mass spectrometry.

Visualize Your Data with Style

You can also visualize amphipathic helices using WinPep! These are important when looking at protein-protein interactions. The software displays subsequences as helical wheels which help spot potential helices with strong amphipathy. It calculates something called the “amphipathic moment” which shows how hydrophilic and hydrophobic amino acids are spread out in a helix. A close-to-zero value means a balanced mix while larger values show an uneven distribution.

Create Hydropathic Plots Easily

An added bonus? You can create hydropathic plots based on a running window average with different window sizes! It uses predefined scales like Kyte and Doolittle or Sweet and Eisenberg. And if you have your own scale in mind, just enter that instead!

If you're also looking into predicting immunogenic epitopes, WinPep allows for that too! Plus, all these plots can be easily copied to other applications using Copy & Paste.

A Real-Life Example: CNGC1 Protein Analysis

For instance, take a look at a hydropathic plot of cyclic nucleotide-gated channel 1 (CNGC1). This protein is similar to some channels found in animals but is from the model plant Arabidopsis thaliana. The plot helps predict its topology—like how many transmembrane helices it has—and gives insight into its unique family of channel proteins!

If you want to check out WinPep yourself for all these amazing features and more, click here!