How is protein pI calculated?

The pI (isoelectric point) refers to the pH at which the net charge of a protein is zero. We calculate the theoretical pI by using the pKa's of amino acids and summing the net charge across the protein at a given pH, searching with our algorithm for the pH at which the net charge is zero.

How is protein molecular weight calculated?

The MW of a protein is calculated by adding up the molecular weights of the amino acids, per standard calculations.

Where do the amino acid hydrophobicity values come from?

The hydrophobicities given are the "Scaled" values from computational log(P) determinations by the "Small Fragment Approach" (see, "Development of Hydrophobicity Parameters to Analyze Proteins Which Bear Post- or Cotranslational Modifications" Black, S.D. and Mould, D.R. (1991) Anal. Biochem. 193, 72-82). The equation used to scale raw log(P) values to the scaled values given is as follows: Scaled Parameters = (Raw Parameters + 2.061)/4.484 .

The work above is summarized here.

How is the instability index calculated? 

Per ProtParam, "a protein whose instability index is smaller than 40 is predicted as stable, a value above 40 predicts that the protein may be unstable". To calculate this, we use the same algorithm as biojava - you can see the specifics here.

How is the extinction coefficient calculated?

The extinction coefficient is calculated by per standard calculations using Beer's Law, via an algorithm from

What do the colors of the amino acids mean? 

We support three coloring schemes. The default is RasMol.

  • RasMol: this coloring scheme is traditional, and groups amino acids by property. In general, polar residues are brighter colors, while non-polar residues appear more subdued.
  • Polarity: yellow means non-polar, green means polar uncharged, red means polar acidic, and blue means polar basic.
  • Hydrophobicity: the residues are colored on a spectrum from red to blue, where red means the most hydrophobic and blue means the most hydrophilic.

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