Peptides

• A warning related with Rcpp was solved
• An error in the mz function related with the aminoacid composition of the peptides used as input was solved

Peptides

NEWS

Peptides v.2.4.2

• C++ code of Charge function was optimized by Luis Pedro Coelho

• aaList function was added by Richel Bilderbeek

Peptides v.2.4.1

• Hidden objects in data files were removed following a CRAN maintainers suggestion
• A bug related with the spaces management in the readXVG function was solved. Thanks to @hongbo-zhu-cn.

Peptides v.2.4

• aaComp function now accepts character lists as input. Thanks to Hemílio Xafranski for 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 fabian.tann@lse.thm.de to report it.

Peptides v.2.2

• The Wimley-White hydrophobicity scales were added thanks to Alexander Komin akomin1@jhu.edu 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 ...

Peptides v. 2.2

Peptides v.2.2

The Wimley-White hydrophobicity scales were added thanks to Alexander Komin akomin1@jhu.edu suggestion. WW scales can be used as:
interfaceScale_pH2: White, Stephen (2006-06-29). “Experimentally Determined Hydrophobicity Scales”. University of California, Irvine. Retrieved 2017-05-25
interfaceScale_pH8: White, Stephen (2006-06-29). “Experimentally Determined Hydrophobicity Scales”. University of California, Irvine. Retrieved 2017-05-25
octanolScale_pH2: White, Stephen (2006-06-29). “Experimentally Determined Hydrophobicity Scales”. University of California, Irvine. Retrieved 2017-05-25
octanolScale_pH8: White, Stephen (2006-06-29). “Experimentally Determined Hydrophobicity Scales”. University of California, Irvine. Retrieved 2017-05-25
oiScale_pH2: White, Stephen (2006-06-29). “Experimentally Determined Hydrophobicity Scales”. University of California, Irvine. Retrieved 2017-05-25
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

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 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 1.1.0

• The kidera function and Kfactors dataset were included.
• A instaindex function bug has been fixed.
• A problem with line breaks in sequences was solved.

Peptides 1.0.3

• A membpos function bug has been fixed.
• The results now are not rounded.
• Hydrophobicity function now can compute the GRAVY index with one of the 38 scales includes in Peptides.
• 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.

Peptides v1.0

Available functions

Code	Function
aacomp	Compute the amino-acid composition of a protein sequence
aindex	Compute the aliphatic index of a protein sequence
boman	Compute the Boman (Potential Protein Interaction) index
charge	Compute the theoretical net charge of a protein sequence
hydrophobicity	Compute the hydrophobicity index
hmoment	Compute the hydrophobic moment of a protein sequence
instaindex	Compute the instability index of a protein sequence
lengthpep	Compute the aminoacid length of a protein sequence
membpos	Compute theoretically the class of a protein sequence
mw	Compute the molecular weight of a protein sequence
pI	Compute the isoelectic point (pI) of a protein sequence
plot.xvg	Plot time series from GROMACS XVG files
read.xvg	Read XVG files from GROMACS molecular dynamics package

Available datasets

Code	Description
H	24 Hydrophobicity values for amino acids form ExPASy "protscale"
Pepdata	A data frame with physicochemical properties and indices from 100 amino-acid sequences (50 antimicrobial and 50 non antimicrobial)
pKscales	9 pKa scales for the side chain of charged amino acids from various sources

News

• RUnit tests
• Vectorized functions
• Different scales in hydrophobicity, charge and pI functions

Peptides v0.4 release

Include functions

Code	Function
aacomp	Compute the amino-acid composition of a protein sequence
aindex	Compute the aliphatic index of a protein sequence
boman	Compute the Boman (Potential Protein Interaction) index
charge	Compute the theoretical net charge of a protein sequence
h	Compute the hydrophobicity index (Eisenberg (1984) scale only)
kd	Compute the hydrophobicity index (Kyte Doolittle scale only)
hmoment	Compute the hydrophobic moment of a protein sequence
instaindex	Compute the instability index of a protein sequence
lengthpep	Compute the aminoacid length of a protein sequence
membpos	Compute theoretically the class of a protein sequence
mw	Compute the molecular weight of a protein sequence
pI	Compute the isoelectic point (pI) of a protein sequence
plot.xvg	Plot time series from GROMACS XVG files
read.xvg	Read XVG files from GROMACS molecular dynamics package

Peptides v0.2 release

Include functions

Code	Function
aacomp	Compute the amino-acid composition of a protein sequence
ai	Compute the aliphatic index of a protein sequence
charge	Compute the theoretical net charge of a protein sequence
kd	Compute the hydrophobicity index (Kyte Doolittle scale only)
mw	Compute the molecular weight of a protein sequence
pI	Compute the isoelectic point (pI) of a protein sequence
plot.xvg	Plot time series from GROMACS XVG files
read.xvg	Read XVG files from GROMACS molecular dynamics package