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Wimley Laboratory ~ PepDraw Help

About the Program: PepDraw is a tool that was developed to facilitate the study of the chemical structure and properties of peptides. It allows users to draw the primary chemical structure of an amino acid sequence and predict some chemical properties such as mass, charge, and hydrophobicity.  PepDraw was designed to be a powerful yet user-friendly tool for peptide analysis. It is especially useful for teaching students about the structure and properties of the amino acids.

PepDraw Web

The latest (and greatest) version of pepdraw is now on the web.


Sequence entry:

A sequence may be entered by typing directly into the sequence entry field or by clicking the buttons in the "Amino Acid Keypad." The program will only read characters that code for the 20 natural amino acids.

Peptide properties:

Properties are generated automatically upon changing the information in the sequence entry field.

  • Sequence 
    The sequence that was analyzed, displayed in single-letter code.
  • Sequence length 
    The number of valid amino acid characters entered by the user.
  • Mass 
    The mass or formula weight is the sum of monoisotopic masses of all amino acid residues in the peptide. This is calculated by adding the atomic masses of all side-chain atoms to the mass of all backbone atoms plus the mass of water.
  • Isoelectric point (pI) 
    The isoelectric point is the pH at which the net charge of a peptide is zero. The calculation of the pI assesses the partial charge of the peptide at various pH values starting from 0 and incrementing 0.01 pH units per step.
  • Net charge 
    The net charge is the sum of positively (basic) and negatively (acidic) charged residues at neutral pH.
  • Hydrophobicity (Wimley-White scale)* 
    Hydrophobicity here is the free energy associated with transitioning a peptide from an aqueous environment to a hydrophobic environment like octanol. The scale used is the Wimley-White scale, an experimentally determined scale, where the hydrophobicity of the peptide is the sum of Wimley-White hydrophobicities. The units of measure is in Kcal per mol. Neutral pH is assumed.
  • Molar extinction coefficient 
    The molar extinction coefficient is a factor used to describe how much light a molecule absorbs. In this case the light is at a wavelength of 280 nm. The most strongly absorbing side chains at this wavelength are tryptophan, tyrosine, and cysteine when it forms disulfide pairs called cystines. The molar extinction is calculated by first counting the number of tryptophans (W), the number of tyrosines (Y), and the number of disulfide bonding pairs (cystines). Then the following formula is used to calculate the first extinction coefficient: W*5500 + Y*1490 + cystines*125. This calculation assumes that all cysteines pair into cystines. The second version assumes that all cysteines are reduced and there are no cystines, thus it is calculated as W*5500 + Y*1490.
  • Peptide structure image 
    The image is in PNG (portable network graphics) format. The images are larger than they appear on-screen. Images can be saved or copied by right-clicking.

Further Questions: Any further questions/concerns/inputs about the program can be emailed to Thomas Freeman at or Hussain Badani at


* S.H. White, W.C. Wimley, Hydrophobic interactions of peptides with membrane interfaces, Biochimica et biophysica acta 1376 (1998) 339-352.