Calculate Indices and Theoretical Physicochemical Properties of Protein Sequences

Includes functions to calculate several physicochemical properties and indices for amino-acid sequences as well as to read and plot 'XVG' output files from the 'GROMACS' molecular dynamics package.


R package to calculate several physicochemical properties and indices for amino-acid sequences as well as to read and plot 'XVG' output files from the 'GROMACS' molecular dynamics package

Install

This package required R version 1.2.2 or higher. If you are using an older version of R you will be prompted to upgrade when you try to install the package.

The official release of Peptides is available on CRAN. To install from CRAN, use the following command:

install.packages("Peptides", dependencies=TRUE)

If you have devtools installed, install the latest stable version this package directly from GitHub:

library(devtools)
install_github("dosorio/Peptides")
library(Peptides)

Available functions

Code Function
aaComp Compute the amino-acid composition of a protein sequence
aaDescriptors Compute 66 descriptors for each amino acid of a protein sequence
aIndex Compute the aliphatic index of a protein sequence
autoCorrelation Compute the auto-correlation index of a protein sequence
autoCovariance Compute the auto-covariance index of a protein sequence
blosumIndices Compute the BLOSUM62 derived indices of a protein sequence
boman Compute the Boman (Potential Protein Interaction) index
charge Compute the theoretical net charge of a protein sequence
crossCovariance Compute the cross-covariance index of a protein sequence
crucianiProperties Compute the Cruciani properties of a protein sequence
fasgaiVectors Compute the FASGAI vectors of a protein sequence
hmoment Compute the hydrophobic moment of a protein sequence
hydrophobicity Compute the hydrophobicity index of a protein sequence
instaIndex Compute the instability index of a protein sequence
kideraFactors Compute the Kidera factors of a protein sequence
lengthpep Compute the aminoacid length of a protein sequence
membpos Compute theoretically the class of a protein sequence
mswhimScores Compute the MS-WHIM scores of a protein sequence
mw Compute the molecular weight of a protein sequence
pI Compute the isoelectic point (pI) of a protein sequence
plotXVG Plot time series from GROMACS XVG files
protFP Compute the protFP descriptors of a protein sequence
readXVG Read XVG files from GROMACS molecular dynamics package
stScales Compute the ST-scales of a protein sequence
tScales Compute the T-scales of a protein sequence
vhseScales Compute the VHSE-scales of a protein sequence
zScales Compute the Z-scales of a protein sequence

Available datasets

Code Description
AAdata Properties, scales and indices for the 20 naturally occurring amino acids from various sources
pepdata A data frame with 21 physicochemical properties and indices from 100 amino-acid sequences (50 antimicrobial and 50 non antimicrobial)

Citation

Osorio, D., Rondon-Villarreal, P. & Torres, R. Peptides: A package for data mining of antimicrobial peptides. The R Journal. 7(1), 4–14 (2015).

D. Osorio, P. Rondón-Villarreal and R. Torres. Peptides: Calculate indices and theoretical physicochemical properties of peptides and protein sequences., 2014. URL: http: //CRAN.R-project.org/package=Peptides. R Package Version 2.2.

News

NEWS

Peptides v.2.3

  • aaComp function now accepts character lists as input. Thanks to Hemílio Xafranski from their suggestion.

Peptides v.2.3

  • A problem with the tScales and tsScales functions was solved. The problem made the return of the functions an empty list. Thanks to Fabian Tann [email protected] to report it.

Peptides v.2.2

  • The Wimley-White hydrophobicity scales were added thanks to Alexander Komin [email protected] suggestion. WW scales can be used as:
  1. interfaceScale_pH2: White, Stephen (2006-06-29). "Experimentally Determined Hydrophobicity Scales". University of California, Irvine. Retrieved 2017-05-25
  2. interfaceScale_pH8: White, Stephen (2006-06-29). "Experimentally Determined Hydrophobicity Scales". University of California, Irvine. Retrieved 2017-05-25
  3. octanolScale_pH2: White, Stephen (2006-06-29). "Experimentally Determined Hydrophobicity Scales". University of California, Irvine. Retrieved 2017-05-25
  4. octanolScale_pH8: White, Stephen (2006-06-29). "Experimentally Determined Hydrophobicity Scales". University of California, Irvine. Retrieved 2017-05-25
  5. oiScale_pH2: White, Stephen (2006-06-29). "Experimentally Determined Hydrophobicity Scales". University of California, Irvine. Retrieved 2017-05-25
  6. oiScale_pH8: White, Stephen (2006-06-29). "Experimentally Determined Hydrophobicity Scales". University of California, Irvine. Retrieved 2017-05-25

Peptides v.2.1

  • The charge and pI functions were rewritten in C++ and an optimization approach was used thanks to Scott McCain (@jspmccain) and Timothée Poisot (@tpoisot) suggestion.

  • An error in zScales function data was solved. Q and E values were wrongly interchanged in v 2.0.

Peptides v.2.0.0

  • All datasets were unified into AAdata

  • All test were migrated to testthat

  • readXVG and plotXVG functions were improved by J. Sebastian Paez

  • kideraFactors output vector was renamed as KF#

  • Now all sequences are checked before to property calculation

  • aaDescriptos, fasgaiVectors, blosumIndices, mswhimScores, zScales, vhseScales, protFP, tScales and stScales functions were added

Peptides v.1.2.2

  • crucianiProperties function was added.

Peptides v.1.2.1

  • Four new functions were added: autoCorrelation, autoCovariance, crossCovariance and crucianiProperties

  • Functions related with XVG files were updated.

  • Documentation was changed to roxygen2

Peptides v.1.1.2

  • All functions were re-vectorized to support set of peptides as input

  • Kidera function now returns all factors in a unique output

Peptides v.1.1.1

  • The mw function now computes the molecular weight using monoisotopic values

  • A problem with blank spaces was solved

Peptides v.1.1.0

  • The kidera function and Kfactors dataset was included.

Peptides v.1.0.4

  • A instaindex function bug has been fixed.

  • A problem with line breaks in sequences was solved.

Peptides v.1.0.3

  • A membpos function bug has been fixed.

  • The results now are not rounded.

Peptides v.1.0.2

  • Hydrophobicity function now can compute the GRAVY index with one of the 38 scales includes in Peptides (*new):

    1. Aboderin: Aboderin, A. A. (1971). An empirical hydrophobicity scale for α-amino-acids and some of its applications. International Journal of Biochemistry, 2(11), 537-544.
    2. AbrahamLeo: Abraham D.J., Leo A.J. Hydrophobicity (delta G1/2 cal). Proteins: Structure, Function and Genetics 2:130-152(1987).
    3. *Argos: Argos, P., Rao, J. K., & Hargrave, P. A. (1982). Structural Prediction of Membrane‐Bound Proteins. European Journal of Biochemistry, 128(2‐3), 565-575.
    4. BlackMould: Black S.D., Mould D.R. Hydrophobicity of physiological L-alpha amino acids. Anal. Biochem. 193:72-82(1991).
    5. BullBreese: Bull H.B., Breese K. Hydrophobicity (free energy of transfer to surface in kcal/mole). Arch. Biochem. Biophys. 161:665-670(1974).
    6. *Casari: Casari, G., & Sippl, M. J. (1992). Structure-derived hydrophobic potential: hydrophobic potential derived from X-ray structures of globular proteins is able to identify native folds. Journal of molecular biology, 224(3), 725-732.
    7. Chothia: Chothia, C. (1976). The nature of the accessible and buried surfaces in proteins. Journal of molecular biology, 105(1), 1-12.
    8. *Cid: Cid, H., Bunster, M., Canales, M., & Gazitúa, F. (1992). Hydrophobicity and structural classes in proteins. Protein engineering, 5(5), 373-375.
    9. Cowan3.4: Cowan R., Whittaker R.G. Hydrophobicity indices at pH 3.4 determined by HPLC. Peptide Research 3:75-80(1990).
    10. Cowan7.5: Cowan R., Whittaker R.G. Hydrophobicity indices at pH 7.5 determined by HPLC. Peptide Research 3:75-80(1990).
    11. Eisenberg: Eisenberg D., Schwarz E., Komarony M., Wall R. Normalized consensus hydrophobicity scale. J. Mol. Biol. 179:125-142(1984).
    12. *Engelman: Engelman, D. M., Steitz, T. A., & Goldman, A. (1986). Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins. Annual review of biophysics and biophysical chemistry, 15(1), 321-353.
    13. *Fasman: Fasman, G. D. (Ed.). (1989). Prediction of protein structure and the principles of protein conformation. Springer.
    14. Fauchere: Fauchere J.-L., Pliska V.E. Hydrophobicity scale (pi-r). Eur. J. Med. Chem. 18:369-375(1983).
    15. *Goldsack: Goldsack, D. E., & Chalifoux, R. C. (1973). Contribution of the free energy of mixing of hydrophobic side chains to the stability of the tertiary structure of proteins. Journal of theoretical biology, 39(3), 645-651.
    16. Guy: Guy H.R. Hydrophobicity scale based on free energy of transfer (kcal/mole). Biophys J. 47:61-70(1985).
    17. HoppWoods: Hopp T.P., Woods K.R. Hydrophilicity. Proc. Natl. Acad. Sci. U.S.A. 78:3824-3828(1981).
    18. Janin: Janin J. Free energy of transfer from inside to outside of a globular protein. Nature 277:491-492(1979).
    19. *Jones: Jones, D. D. (1975). Amino acid properties and side-chain orientation in proteins: a cross correlation approach. Journal of theoretical biology, 50(1), 167-183.
    20. *Juretic: Juretic, D., Lucic, B., Zucic, D., & Trinajstic, N. (1998). Protein transmembrane structure: recognition and prediction by using hydrophobicity scales through preference functions. Theoretical and computational chemistry, 5, 405-445.
    21. *Kidera: Kidera, A., Konishi, Y., Oka, M., Ooi, T., & Scheraga, H. A. (1985). Statistical analysis of the physical properties of the 20 naturally occurring amino acids. Journal of Protein Chemistry, 4(1), 23-55.
    22. *Kuhn: Kuhn, L. A., Swanson, C. A., Pique, M. E., Tainer, J. A., & Getzoff, E. D. (1995). Atomic and residue hydrophilicity in the context of folded protein structures. Proteins: Structure, Function, and Bioinformatics, 23(4), 536-547.
    23. KyteDoolittle: Kyte J., Doolittle R.F. Hydropathicity. J. Mol. Biol. 157:105-132(1982).
    24. *Levitt: Levitt, M. (1976). A simplified representation of protein conformations for rapid simulation of protein folding. Journal of molecular biology, 104(1), 59-107.
    25. Manavalan: Manavalan P., Ponnuswamy Average surrounding hydrophobicity. P.K. Nature 275:673-674(1978).
    26. Miyazawa: Miyazawa S., Jernigen R.L. Hydrophobicity scale (contact energy derived from 3D data). Macromolecules 18:534-552(1985).
    27. Parker: Parker J.M.R., Guo D., Hodges R.S. Hydrophilicity scale derived from HPLC peptide retention times. Biochemistry 25:5425-5431(1986).
    28. *Ponnuswamy: Ponnuswamy, P. K. (1993). Hydrophobic charactesristics of folded proteins. Progress in biophysics and molecular biology, 59(1), 57-103.
    29. *Prabhakaran: Prabhakaran, M. (1990). The distribution of physical, chemical and conformational properties in signal and nascent peptides. Biochem. J, 269, 691-696.
    30. Rao: Rao M.J.K., Argos P. Membrane buried helix parameter. Biochim. Biophys. Acta 869:197-214(1986).
    31. Rose: Rose G.D., Geselowitz A.R., Lesser G.J., Lee R.H., Zehfus M.H. Mean fractional area loss (f) [average area buried/standard state area]. Science 229:834-838(1985)
    32. Roseman: Roseman M.A. Hydrophobicity scale (pi-r). J. Mol. Biol. 200:513-522(1988).
    33. Sweet: Sweet R.M., Eisenberg D. Optimized matching hydrophobicity (OMH). J. Mol. Biol. 171:479-488(1983).
    34. Tanford: Tanford C. Hydrophobicity scale (Contribution of hydrophobic interactions to the stability of the globular conformation of proteins). J. Am. Chem. Soc. 84:4240-4274(1962).
    35. Welling: Welling G.W., Weijer W.J., Van der Zee R., Welling-Wester S. Antigenicity value X 10. FEBS Lett. 188:215-218(1985).
    36. Wilson: Wilson K.J., Honegger A., Stotzel R.P., Hughes G.J. Hydrophobic constants derived from HPLC peptide retention times. Biochem. J. 199:31-41(1981).
    37. Wolfenden: Wolfenden R.V., Andersson L., Cullis P.M., Southgate C.C.F. Hydration potential (kcal/mole) at 25C. Biochemistry 20:849-855(1981).
    38. *Zimmerman: Zimmerman, J. M., Eliezer, N., & Simha, R. (1968). The characterization of amino acid sequences in proteins by statistical methods. Journal of theoretical biology, 21(2), 170-201.
  • The mw function has been fixed to give the same result as ExPASy pI/mw tool.

  • The hmoment function is now vectorized and allow adjust the windows size. (thanks to an anonymous reviewer of RJournal).

  • The pepdata dataset and the variable name are now unified to lowercases.

  • The seqinr package dependency was removed.

Reference manual

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install.packages("Peptides")

2.4 by Daniel Osorio, a year ago


https://github.com/dosorio/Peptides/


Browse source code at https://github.com/cran/Peptides


Authors: Daniel Osorio [aut, cre] , Paola Rondon-Villarreal [aut, ths] , Rodrigo Torres [aut, ths] , J. Sebastian Paez [ctb]


Documentation:   PDF Manual  


GPL-2 license


Imports Rcpp

Suggests testthat

Linking to Rcpp


See at CRAN