HydrophobicityProfile Class Reference

This class is used for hydrophobicity profiling of peptides. More...

#include <OpenMS/CHEMISTRY/HydrophobicityProfile.h>

Public Member Functions
double	computeGRAVY (const AASequence &seq) const
	Calculates the GRAVY score.
std::vector< double >	computeProfile (const AASequence &seq, const HydrophobicityScaleMethod scale=HydrophobicityScaleMethod::KYTE_DOOLITTLE) const
	Calculates hydrophobicity profile per residue.
std::vector< double >	computeWindowedProfile (const AASequence &seq, const Size window_size=7, const HydrophobicityScaleMethod scale=HydrophobicityScaleMethod::KYTE_DOOLITTLE) const
	Calculates windowed hydrophobicity profile.
std::vector< double >	computeHydrophobicMoment (const AASequence &seq, const Size window_size=11, const double angle=100.0) const
	Calculates hydrophobic moments.

Detailed Description

This class is used for hydrophobicity profiling of peptides.

The possible scales are listed here: HydrophobicityScaleMethod

References for the hydrophobicity scales:

• Kyte J, Doolittle RF. A simple method for displaying the hydropathic character of a protein. J Mol Biol. 1982 May 5;157(1):105-32. doi: 10.1016/0022-2836(82)90515-0. PMID: 7108955.
• Eisenberg D, Schwarz E, Komaromy M, Wall R. Analysis of membrane and surface protein sequences with the hydrophobic moment plot. J Mol Biol. 1984 Oct 15;179(1):125-42. doi: 10.1016/0022-2836(84)90309-7. PMID: 6502707.
• T.P. Hopp, & K.R. Woods, Prediction of protein antigenic determinants from amino acid sequences., Proc. Natl. Acad. Sci. U.S.A. 78 (6) 3824-3828, https://doi.org/10.1073/pnas.78.6.3824 (1981).
• Henry B. Bull, Keith Breese, Surface tension of amino acid solutions: A hydrophobicity scale of the amino acid residues, Archives of Biochemistry and Biophysics, Volume 161, Issue 2, 1974, Pages 665-670, ISSN 0003-9861, https://doi.org/10.1016/0003-9861(74)90352-X. (https://www.sciencedirect.com/science/article/pii/000398617490352X)
• Black SD, Mould DR. Development of hydrophobicity parameters to analyze proteins which bear post- or cotranslational modifications. Anal Biochem. 1991 Feb 15;193(1):72-82. doi: 10.1016/0003-2697(91)90045-u. PMID: 2042744.
• Guy, H. R. (1985). Amino acid side-chain partition energies and distribution of residues in soluble proteins. Biophysical journal, 47(1), 61-70.

Paper for calculating the hydrophobic moments (Eisenberg et al. 1984):

• Eisenberg D, Schwarz E, Komaromy M, Wall R. Analysis of membrane and surface protein sequences with the hydrophobic moment plot. J Mol Biol. 1984 Oct 15;179(1):125-42. doi: 10.1016/0022-2836(84)90309-7. PMID: 6502707.
• Eisenberg D, Weiss RM, Terwilliger TC. The hydrophobic moment detects periodicity in protein hydrophobicity. Proc Natl Acad Sci U S A. 1984 Jan;81(1):140-4. doi: 10.1073/pnas.81.1.140. PMID: 6582470; PMCID: PMC344626.

Referenced code for calculating the hydrophobic moment of a windowed peptide
R package R.Peptides: https://github.com/dosorio/Peptides/blob/master/R/hmoment.R

Member Function Documentation

computeGRAVY()

double computeGRAVY

(

const AASequence &

seq

)

const

Calculates the GRAVY score.

Parameters

seq	The amino acid sequence for which to calculate the GRAVY score

Returns

The GRAVY score of a given peptide

Exceptions

Exception::InvalidValue

Throws an exception if the sequence is empty or contains invalid symbols (sequence can only contain the standard 20 Amino acids)

computeHydrophobicMoment()

std::vector< double > computeHydrophobicMoment	(	const AASequence &	seq,
		const Size	window_size = 11,
		const double	angle = 100.0
	)		const

Calculates hydrophobic moments.

Parameters

seq	The Amino acid sequence
window_size	The size of the sliding window for the calculation
angle	The angle to use: 100 for alpha-helices, 160 for beta-sheets, other angles can be used

Returns

A vector which contains the hydrophobic moment for each window

Exceptions

Exception::InvalidValue	Throws an exception if the sequence is empty or contains invalid symbols (sequence can only contain the standard 20 Amino acids)
Exception::InvalidSize	Throws an exception when the window size is 0

Warning

When the window size is larger than the sequence the window size will be clamped to the sequence length

computeProfile()

std::vector< double > computeProfile	(	const AASequence &	seq,
		const HydrophobicityScaleMethod	scale = HydrophobicityScaleMethod::KYTE_DOOLITTLE
	)		const

Calculates hydrophobicity profile per residue.

Parameters

seq	The amino acid sequence for which to calculate the profile
scale	The scale to use for the calculation

Returns

A vector which contains the hydrophobicity value for each amino acid

Exceptions

Exception::InvalidValue

Throws an exception if the sequence is empty or contains invalid symbols (sequence can only contain the standard 20 Amino acids) or when an unknown scale is used

computeWindowedProfile()

std::vector< double > computeWindowedProfile	(	const AASequence &	seq,
		const Size	window_size = 7,
		const HydrophobicityScaleMethod	scale = HydrophobicityScaleMethod::KYTE_DOOLITTLE
	)		const

Calculates windowed hydrophobicity profile.

Parameters

seq	The Amino acid Sequence for which to calculate the profile
window_size	The size of the sliding window for the calculation
scale	The scale to use for the calculation

Returns

A vector which contains the average hydrophobicity for each window

Exceptions

Exception::InvalidValue	Throws an exception if the sequence is empty or contains invalid symbols (sequence can only contain the standard 20 Amino acids) or when an unknown scale is used
Exception::InvalidSize	Throws an exception when the window size is 0

Warning

When the window size is larger than the sequence the window size will be clamped to the sequence length