Recipe 2.3. Computing biochemical properties in peptides

You want to estimate the isoelectric point or the partial charge in peptides.

The BioPolymerUtils class provides methods to estimate biochemical properties in peptide or proteins:

String seq = 
	new String("mvhltpeeksavtalwgkvnvdevggealgrllvvypwtq"
		+ "rffesfgdlstpdavmgnpkvkahgkkvlgafsdglahld"
		+ "nlkgtfatlselhcdklhvdpenfrllgnvlvcvpahhfg"
		+ "keftppvqaayqkvvagvanalahkyh").toUpperCase();
		
Peptide peptide = new Peptide.Builder(seq).build();

// default gravy method
float score = BioPolymerUtils.getGravyScore(sequence);
		Assert.assertEquals(-0.023, score, 0.001);

// gravy "kyledoolittle" method
score = BioPolymerUtils.getGravyScore(sequence, 
	AAHydropathyManager.newInstance("kyledoolittle"));
Assert.assertEquals(-0.023, score, 0.001);

peptide = new Peptide.Builder("QEAYEGK").build();
Assert.assertEquals(4.54, BioPolymerUtils.getIsoelectricPoint(peptide), 0.01);

final float score = BioPolymerUtils.getGravyScore(peptide);
Assert.assertEquals(-0.023, score, 0.001);