diff --git a/DESCRIPTION b/DESCRIPTION index fb05cfd..eae97c7 100755 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,10 +1,10 @@ Package: Peptides -Version: 1.0.2 -Date: 2014-11-15 -Title: Calculate indices and theoretical physicochemical properties of peptides and protein sequences +Version: 1.0.3 +Date: 2014-12-14 +Title: Calculate Indices and Theoretical Properties of Protein Sequences Author: Daniel Osorio, Paola Rondon-Villarreal and Rodrigo Torres. Maintainer: Daniel Osorio URL: https://github.com/dosorio/Peptides/ Suggests: RUnit -Description: Calculate physicochemical properties and indices from aminoacid sequences of peptides and proteins. Include also utilities for read and plot GROMACS output files. +Description: Calculate physicochemical properties and indices from amino-acid sequences of peptides and proteins. Include also the option to read and plot XVG output files from GROMACS molecular dynamics package. License: GPL-2 diff --git a/NEWS b/NEWS new file mode 100644 index 0000000..d317287 --- /dev/null +++ b/NEWS @@ -0,0 +1,55 @@ +NEWS +==== + +**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. diff --git a/R/aindex.R b/R/aindex.R index 394c8a2..b256ef1 100755 --- a/R/aindex.R +++ b/R/aindex.R @@ -14,5 +14,5 @@ aindex<-function(seq){ # and of Leu/Ile side chains (b = 3.9) to the side chain of alanine. # Return the result as percentage rounded to 2 decimals - round(sum(c(p["A"],(2.9*p["V"]),3.9*p[c("L","I")]),na.rm=T)*100,2) + sum(c(p["A"],(2.9*p["V"]),3.9*p[c("L","I")]),na.rm=T)*100 } \ No newline at end of file diff --git a/R/hmoment.R b/R/hmoment.R index 76c72e2..6c1b8fe 100755 --- a/R/hmoment.R +++ b/R/hmoment.R @@ -2,24 +2,25 @@ # This function compute the hmoment based on Eisenberg, D., Weiss, R. M., & Terwilliger, T. C. (1984). # The hydrophobic moment detects periodicity in protein hydrophobicity. # Proceedings of the National Academy of Sciences of the United States of America, 81(1), 140–4. +# This function was written by an anonymous reviewer of the RJournal hmoment<-function(seq,angle=100,window=11){ - # Load hydrophobicity scale + # Loading hydrophobicity scale data(H,envir = environment()) + H<-H h<-H[["Eisenberg"]] - # Spliting the sequence + # Splitting the sequence in amino acids aa<-strsplit(toupper(seq),"")[[1]] window<-min(length(aa),window) - # Setting the sequences + # Setting the sequence length pep<-embed(aa,window) - # Evaluating angles and functions + # Applying the hmoment function to each amino acids window angle<- angle*(pi/180)*1:window vcos<-h[t(pep)]*cos(angle) vsin<-h[t(pep)]*sin(angle) dim(vcos)<-dim(vsin)<-dim(t(pep)) - vcos<-colSums(vcos) - vsin<-colSums(vsin) - # Applying the moment function to each 10 amino acids window + vcos<-colSums(vcos,na.rm = TRUE) + vsin<-colSums(vsin,na.rm = TRUE) # Return the max value max(sqrt(vsin*vsin + vcos*vcos)/window) } diff --git a/R/hydrophobicity.R b/R/hydrophobicity.R index 8edbfe0..448e389 100755 --- a/R/hydrophobicity.R +++ b/R/hydrophobicity.R @@ -6,16 +6,13 @@ # Journal of Molecular Biology, 157(1), 105–32. hydrophobicity<-function(seq,scale="KyteDoolittle"){ - # Setting the hydrophobicity scale - M<-c("KyteDoolittle","AbrahamLeo", "BullBreese", "Guy", "Miyazawa", "Roseman", "Wolfenden", - "Wilson", "Cowan3.4", "Aboderin", "Sweet", "Eisenberg", "HoppWoods", "Manavalan", - "BlackMould", "Fauchere", "Janin", "Rao", "Tanford", "Cowan7.5", "Chothia", - "Rose") - scale<-match.arg(scale,M) # Loading hydrophobicity scales data(H, envir = environment()) H<-H + # Setting the hydrophobicity scale + M<-names(H) + scale<-match.arg(scale,M) # Sum the hydrophobicity of each amino acid and divide them between the sequence length # Return the GRAVY value - sum(H[[scale]][strsplit(seq,"")[[1]]])/nchar(seq) + sum(H[[scale]][strsplit(seq,"")[[1]]],na.rm = TRUE)/nchar(seq) } diff --git a/R/membpos.R b/R/membpos.R index d732384..b02b427 100755 --- a/R/membpos.R +++ b/R/membpos.R @@ -5,12 +5,8 @@ membpos<-function(seq,angle=100){ # Setting input length - aa<-strsplit(toupper(seq),"")[[1]] - window<-min(length(aa),11) - pep<-character(nchar(seq)-window) - for (i in 1: (nchar(seq)-window)){ - pep[i]<-paste(aa[i:(i+window)],collapse = "") - } + window<-min(nchar(seq),11) + pep<-substring(toupper(seq),(window):nchar(seq),first = 1:((nchar(seq)-window)+1)) # Compute the hmoment and hydrophobicity for each amino acid window data<-as.data.frame(matrix(nrow = length(pep),ncol = 5)) data[,1]<-pep diff --git a/README.md b/README.md index 65d5658..7d12281 100755 --- a/README.md +++ b/README.md @@ -1,10 +1,10 @@ Peptides ======== -R package to calculate indices and theoretical physicochemical properties of peptides and protein sequences. Include also utilities for read and plot GROMACS output files .XVG +R package to calculate indices and theoretical physicochemical properties of peptides and protein sequences. Include also the option to read and plot XVG output files from the GROMACS molecular dynamics package. Install ------- -This package required R version 2.10 or higher. If you are using an older version of R you will be prompted to upgrade when you try to install the package. +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: ``` @@ -38,17 +38,17 @@ Available functions |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 | +|plot.xvg | Plot time series from GROMACS XVG files | |read.xvg | Read XVG files from GROMACS molecular dynamics package | Available datasets ------------------- | Code | Description | |:----------- |:------------| -|H | 22 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) | +|H | 38 Hydrophobicity values for amino acids form various sources | +|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 | Citation -------- -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 1.0. +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 1.0.3. diff --git a/data/H.RData b/data/H.RData index 769adee..d35e5c2 100644 Binary files a/data/H.RData and b/data/H.RData differ diff --git a/data/Pepdata.RData b/data/Pepdata.RData deleted file mode 100644 index 4c417e1..0000000 Binary files a/data/Pepdata.RData and /dev/null differ diff --git a/data/pKscales.RData b/data/pKscales.RData index b0df449..1ab18ac 100644 Binary files a/data/pKscales.RData and b/data/pKscales.RData differ diff --git a/data/pepdata.RData b/data/pepdata.RData new file mode 100644 index 0000000..624fe40 Binary files /dev/null and b/data/pepdata.RData differ diff --git a/inst/tests/runit.pI.R b/inst/tests/runit.pI.R index d6f5d44..34063f4 100644 --- a/inst/tests/runit.pI.R +++ b/inst/tests/runit.pI.R @@ -5,8 +5,8 @@ test.pI<- function(){ # Theoretical pI: 9.88 # CHECK pI VALUE - checkEquals(pI("QWGRRCCGWGPGRRYCVRWC","Bje"),9.88) + checkEquals(pI("QWGRRCCGWGPGRRYCVRWC","Bjellqvist"),9.88,tolerance = 0.01) # CHECK OUTPUT CLASS - checkTrue(is.numeric(pI("QWGRRCCGWGPGRRYCVRWC","Bje"))) + checkTrue(is.numeric(pI("QWGRRCCGWGPGRRYCVRWC","Bjellqvist"))) } \ No newline at end of file diff --git a/man/AAcomp.Rd b/man/AAcomp.Rd index 83064aa..89900b6 100755 --- a/man/AAcomp.Rd +++ b/man/AAcomp.Rd @@ -54,13 +54,13 @@ aacomp("KWKLFKKIGIGKFLHSAKKFX") ## Output # Number Mole\% -# Tiny 4 19.05 -# Small 4 19.05 -# Aliphatic 5 23.81 -# Aromatic 5 23.81 -# Non Polar 11 52.38 -# Polar 9 42.86 -# Charged 8 38.10 -# Basic 8 38.10 -# Acidic 0 0.00 +# Tiny 4 19.048 +# Small 4 19.048 +# Aliphatic 5 23.810 +# Aromatic 5 23.810 +# NonPolar 11 52.381 +# Polar 9 42.857 +# Charged 8 38.095 +# Basic 8 38.095 +# Acidic 0 0.000 } diff --git a/man/Boman.Rd b/man/Boman.Rd index 9ed7324..01aa8f2 100755 --- a/man/Boman.Rd +++ b/man/Boman.Rd @@ -28,5 +28,5 @@ Radzicka, A., & Wolfenden, R. (1988). Comparing the polarities of the amino acid # BOMAN INDEX -1.24 boman("FLPVLAGLTPSIVPKLVCLLTKKC") -# [1] -1.24 +# [1] -1.235833 } diff --git a/man/MW.Rd b/man/MW.Rd index 9804e8e..112ff80 100755 --- a/man/MW.Rd +++ b/man/MW.Rd @@ -31,5 +31,5 @@ Chicago # Theoretical pI/Mw: 9.88 / 2485.91 mw("QWGRRCCGWGPGRRYCVRWC") -# [1] 2485.9 +# [1] 2485.911 } \ No newline at end of file diff --git a/man/Peptides-package.Rd b/man/Peptides-package.Rd index 629f80e..a1fcab8 100755 --- a/man/Peptides-package.Rd +++ b/man/Peptides-package.Rd @@ -2,18 +2,18 @@ \alias{Peptides} \docType{package} \title{ -Calculate indices and theoretical physicochemical properties of peptides and proteins sequences. +Calculate Indices and Theoretical Properties of Protein Sequences } \description{ -Calculate physicochemical properties and indices from amino acid sequences of peptides -and proteins. Include also utilities for read and plot GROMACS output files .XVG. +Calculate physicochemical properties and indices from amino-acid sequences of peptides +and proteins. Include also the option to read and plot XVG output files from GROMACS molecular dynamics package. } \details{ \tabular{ll}{ Package: \tab Peptides\cr Type: \tab Package\cr -Version: \tab 1.0.2\cr -Date: \tab 2014-11-11\cr +Version: \tab 1.0.3\cr +Date: \tab 2014-12-12\cr License: \tab GPL-2\cr } } diff --git a/man/aindex.Rd b/man/aindex.Rd index f8e1576..2886f8c 100755 --- a/man/aindex.Rd +++ b/man/aindex.Rd @@ -5,14 +5,14 @@ %% ~~function to do ... ~~ } \description{ -This function calculates the Ikai (1980) aliphatic index of a protein. The aindex is defined as the relative volume occupied by aliphatic side chains (Alanine, Valine, Isoleucine, and Leucine). It may be regarded as a positive factor for the increase of thermostability of globular proteins. +This function calculates the Ikai (1980) aliphatic index of a protein. The \code{aindex} is defined as the relative volume occupied by aliphatic side chains (Alanine, Valine, Isoleucine, and Leucine). It may be regarded as a positive factor for the increase of thermostability of globular proteins. } \usage{ aindex(seq) } %- maybe also 'usage' for other objects documented here. \arguments{ - \item{seq}{amino acid sequence string in upper case} + \item{seq}{amino acid sequence string} } \references{ @@ -22,7 +22,6 @@ Ikai (1980). Thermostability and aliphatic index of globular proteins. Journal o \examples{ # COMPARED TO ExPASy ALIPHATIC INDEX # http://web.expasy.org/protparam/ - # SEQUENCE: SDKEVDEVDAALSDLEITLE # Aliphatic index: 117.00 diff --git a/man/charge.Rd b/man/charge.Rd index f1d5cce..a9eb8c2 100755 --- a/man/charge.Rd +++ b/man/charge.Rd @@ -5,7 +5,7 @@ %% ~~function to do ... ~~ } \description{ -This function computes the net charge of a protein sequence based on the Henderson-Hasselbalch equation described by Moore, D. S. (1985). The net charge can be calculated at defined pH using one of the 9 pKa scales availables: Bjellqvist, EMBOSS, Murray, Sillero, Solomon, Stryer, Lehninger, Dawson or Rodwell +This function computes the net charge of a protein sequence based on the Henderson-Hasselbalch equation described by Moore, D. S. (1985). The net charge can be calculated at defined pH using one of the 9 pKa scales availables: \code{Bjellqvist}, \code{Dawson}, \code{EMBOSS}, \code{Lehninger}, \code{Murray}, \code{Rodwell}, \code{Sillero}, \code{Solomon} or \code{Stryer}. } \usage{ charge(seq, pH, pKscale) @@ -14,7 +14,7 @@ charge(seq, pH, pKscale) \arguments{ \item{seq}{amino acid sequence as string} \item{pH}{pH value} - \item{pKscale}{a character string specifying the pKa scale to be used; must be one of \code{"Bjellqvist"}, \code{"EMBOSS"}, \code{"Murray"}, \code{"Sillero"}, \code{"Solomon"}, \code{"Stryer"}, \code{"Lehninger"}, \code{"Dawson"} or \code{"Rodwell"}} + \item{pKscale}{a character string specifying the pKa scale to be used; must be one of \code{"Bjellqvist"}, \code{"Dawson"}, \code{"EMBOSS"}, \code{"Lehninger"}, \code{"Murray"}, \code{"Rodwell"}, \code{"Sillero"}, \code{"Solomon"} or \code{"Stryer"}} } \references{ @@ -22,10 +22,16 @@ Kiraga, J. (2008) Analysis and computer simulations of variability of isoelectri Bjellqvist, B., Hughes, G.J., Pasquali, Ch., Paquet, N., Ravier, F., Sanchez, J.Ch., Frutige,r S., Hochstrasser D. (1993) The focusing positions of polypeptides in immobilized pH gradients can be predicted from their amino acid sequences. Electrophoresis, 14:1023-1031. +Dawson, R. M. C.; Elliot, D. C.; Elliot, W. H.; Jones, K. M. Data for biochemical research. Oxford University Press, 1989; p. 592. + EMBOSS data are from http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/iep.html. +Nelson, D. L.; Cox, M. M. Lehninger Principles of Biochemistry, Fourth Edition; W. H. Freeman, 2004; p. 1100. + Murray, R.K., Granner, D.K., Rodwell, V.W. (2006) Harper's illustrated Biochemistry. 27th edition. Published by The McGraw-Hill Companies. +Rodwell, J. Heterogeneity of component bands in isoelectric focusing patterns. Analytical Biochemistry, 1982, 119 (2), 440-449. + Sillero, A., Maldonado, A. (2006) Isoelectric point determination of proteins and other macromolecules: oscillating method. Comput Biol Med., 36:157-166. Solomon, T.W.G. (1998) Fundamentals of Organic Chemistry, 5th edition. Published by Wiley. @@ -40,23 +46,23 @@ Stryer L. (1999) Biochemia. czwarta edycja. Wydawnictwo Naukowe PWN. # Charge = 3.0 charge(seq="FLPVLAGLTPSIVPKLVCLLTKKC",pH=7, pKscale="Bjellqvist") -# [1] 2.737 +# [1] 2.737303 charge(seq="FLPVLAGLTPSIVPKLVCLLTKKC",pH=7, pKscale="EMBOSS") -# [1] 2.914 +# [1] 2.914112 charge(seq="FLPVLAGLTPSIVPKLVCLLTKKC",pH=7, pKscale="Murray") -# [1] 2.908 +# [1] 2.907541 charge(seq="FLPVLAGLTPSIVPKLVCLLTKKC",pH=7, pKscale="Sillero") -# [1] 2.920 +# [1] 2.919812 charge(seq="FLPVLAGLTPSIVPKLVCLLTKKC",pH=7, pKscale="Solomon") -# [1] 2.844 +# [1] 2.844406 charge(seq="FLPVLAGLTPSIVPKLVCLLTKKC",pH=7, pKscale="Stryer") -# [1] 2.877 +# [1] 2.876504 charge(seq="FLPVLAGLTPSIVPKLVCLLTKKC",pH=7, pKscale="Lehninger") -# [1] 2.873 +# [1] 2.87315 charge(seq="FLPVLAGLTPSIVPKLVCLLTKKC",pH=7, pKscale="Dawson") -# [1] 2.844 +# [1] 2.844406 charge(seq="FLPVLAGLTPSIVPKLVCLLTKKC",pH=7, pKscale="Rodwell") -# [1] 2.820 +# [1] 2.819755 # COMPARED TO YADAMP # http://yadamp.unisa.it/showItem.aspx?yadampid=845&x=0,7055475 @@ -66,13 +72,13 @@ charge(seq="FLPVLAGLTPSIVPKLVCLLTKKC",pH=7, pKscale="Rodwell") # CHARGE pH9: 1.09 charge(seq="FLPVLAGLTPSIVPKLVCLLTKKC",pH=5, pKscale="EMBOSS") -# [1] 3.037 +# [1] 3.037398 charge(seq="FLPVLAGLTPSIVPKLVCLLTKKC",pH=7, pKscale="EMBOSS") -# [1] 2.914 +# [1] 2.914112 charge(seq="FLPVLAGLTPSIVPKLVCLLTKKC",pH=9, pKscale="EMBOSS") -# [1] 0.718 +# [1] 0.7184524 # JUST ONE COMMAND charge(seq="FLPVLAGLTPSIVPKLVCLLTKKC",pH=seq(from = 5,to = 9,by = 2), pKscale="EMBOSS") -# [1] 3.037 2.914 0.718 +# [1] 3.0373984 2.9141123 0.7184524 } \ No newline at end of file diff --git a/man/h.Rd b/man/h.Rd index 67e946a..76a24c2 100644 --- a/man/h.Rd +++ b/man/h.Rd @@ -1,64 +1,109 @@ \name{H} \alias{H} \docType{data} -\title{22 Hydrophobicity values for amino acids form ExPASy "protscale" +\title{38 Hydrophobicity values for amino acids from various sources %% ~~ data name/kind ... ~~ } -\description{A list with 22 hydrophobicity scales form ExPASy "protscale" +\description{A list with 38 Hydrophobicity scales for amino acids from various sources" %% ~~ A concise (1-5 lines) description of the dataset. ~~ } \usage{data(H)} \format{ - A list with 22 Hydrophobicity scales. + A list with 38 Hydrophobicity scales. } \details{ Hydrophobicity scales are values that define relative hydrophobicity of amino acid residues. } \source{ -ExPASy-Protscale (http://web.expasy.org/protscale/)} +ExPASy-Protscale (http://web.expasy.org/protscale/) + +AAIndex Database (http://www.genome.jp/aaindex/)} \references{ -Gasteiger, E., Hoogland, C., Gattiker, A., Wilkins, M. R., Appel, R. D., & Bairoch, A. (2005). Protein identification and analysis tools on the ExPASy server. In The proteomics protocols handbook (pp. 571-607). Humana Press. +Aboderin, A. A. (1971). An empirical hydrophobicity scale for alpha-amino-acids and some of its applications. International Journal of Biochemistry, 2(11), 537-544. -Eisenberg D., Schwarz E., Komarony M., Wall R. Normalized consensus hydrophobicity scale. J. Mol. Biol. 179:125-142(1984). +Abraham D.J., Leo A.J. Hydrophobicity (delta G1/2 cal). Proteins: Structure, Function and Genetics 2:130-152(1987). -Sweet R.M., Eisenberg D. Optimized matching hydrophobicity (OMH). J. Mol. Biol. 171:479-488(1983). +Argos, P., Rao, J. K., & Hargrave, P. A. (1982). Structural Prediction of Membrane-Bound Proteins. European Journal of Biochemistry, 128(2-3), 565-575. -Hopp T.P., Woods K.R. Hydrophilicity. Proc. Natl. Acad. Sci. U.S.A. 78:3824-3828(1981). +Black S.D., Mould D.R. Hydrophobicity of physiological L-alpha amino acids. Anal. Biochem. 193:72-82(1991). -Kyte J., Doolittle R.F. Hydropathicity. J. Mol. Biol. 157:105-132(1982). +Bull H.B., Breese K. Hydrophobicity (free energy of transfer to surface in kcal/mole). Arch. Biochem. Biophys. 161:665-670(1974). -Manavalan P., Ponnuswamy Average surrounding hydrophobicity. P.K. Nature 275:673-674(1978). +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. -Abraham D.J., Leo A.J. Hydrophobicity (delta G1/2 cal). Proteins: Structure, Function and Genetics 2:130-152(1987). +Chothia, C. (1976). The nature of the accessible and buried surfaces in proteins. Journal of molecular biology, 105(1), 1-12. -Black S.D., Mould D.R. Hydrophobicity of physiological L-alpha amino acids. Anal. Biochem. 193:72-82(1991). +Cid, H., Bunster, M., Canales, M., & Gazitua, F. (1992). Hydrophobicity and structural classes in proteins. Protein engineering, 5(5), 373-375. + +Cowan R., Whittaker R.G. Hydrophobicity indices at pH 3.4 determined by HPLC. Peptide Research 3:75-80(1990). -Bull H.B., Breese K. Hydrophobicity (free energy of transfer to surface in kcal/mole). Arch. Biochem. Biophys. 161:665-670(1974). +Cowan R., Whittaker R.G. Hydrophobicity indices at pH 7.5 determined by HPLC. Peptide Research 3:75-80(1990). + +Eisenberg D., Schwarz E., Komarony M., Wall R. Normalized consensus hydrophobicity scale. J. Mol. Biol. 179:125-142(1984). + +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. + +Fasman, G. D. (Ed.). (1989). Prediction of protein structure and the principles of protein conformation. Springer. Fauchere J.-L., Pliska V.E. Hydrophobicity scale (pi-r). Eur. J. Med. Chem. 18:369-375(1983). +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. + Guy H.R. Hydrophobicity scale based on free energy of transfer (kcal/mole). Biophys J. 47:61-70(1985). +Hopp T.P., Woods K.R. Hydrophilicity. Proc. Natl. Acad. Sci. U.S.A. 78:3824-3828(1981). + Janin J. Free energy of transfer from inside to outside of a globular protein. Nature 277:491-492(1979). +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. + +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. + +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. + +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. + +Kyte J., Doolittle R.F. Hydropathicity. J. Mol. Biol. 157:105-132(1982). + +Levitt, M. (1976). A simplified representation of protein conformations for rapid simulation of protein folding. Journal of molecular biology, 104(1), 59-107. + +Manavalan P., Ponnuswamy Average surrounding hydrophobicity. P.K. Nature 275:673-674(1978). + Miyazawa S., Jernigen R.L. Hydrophobicity scale (contact energy derived from 3D data). Macromolecules 18:534-552(1985). +Parker J.M.R., Guo D., Hodges R.S. Hydrophilicity scale derived from HPLC peptide retention times. Biochemistry 25:5425-5431(1986). + +Ponnuswamy, P. K. (1993). Hydrophobic charactesristics of folded proteins. Progress in biophysics and molecular biology, 59(1), 57-103. + +Prabhakaran, M. (1990). The distribution of physical, chemical and conformational properties in signal and nascent peptides. Biochem. J, 269, 691-696. + Rao M.J.K., Argos P. Membrane buried helix parameter. Biochim. Biophys. Acta 869:197-214(1986). +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) + Roseman M.A. Hydrophobicity scale (pi-r). J. Mol. Biol. 200:513-522(1988). +Sweet R.M., Eisenberg D. Optimized matching hydrophobicity (OMH). J. Mol. Biol. 171:479-488(1983). + 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). -Wolfenden R.V., Andersson L., Cullis P.M., Southgate C.C.F. Hydration potential (kcal/mole) at 25C. Biochemistry 20:849-855(1981). +Welling G.W., Weijer W.J., Van der Zee R., Welling-Wester S. Antigenicity value X 10. FEBS Lett. 188:215-218(1985). 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). -Parker J.M.R., Guo D., Hodges R.S. Hydrophilicity scale derived from HPLC peptide retention times. Biochemistry 25:5425-5431(1986). +Wolfenden R.V., Andersson L., Cullis P.M., Southgate C.C.F. Hydration potential (kcal/mole) at 25C. Biochemistry 20:849-855(1981). + +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. + +Nakai, K., Kidera, A., and Kanehisa, M.; Cluster analysis of amino acid indices for prediction of protein structure and function. Protein Eng. 2, 93-100 (1988). + +Tomii, K. and Kanehisa, M.; Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins. Protein Eng. 9, 27-36 (1996). -Cowan R., Whittaker R.G. Hydrophobicity indices at ph 3.4 determined by HPLC. Peptide Research 3:75-80(1990). +Kawashima, S., Ogata, H., and Kanehisa, M.; AAindex: amino acid index database. Nucleic Acids Res. 27, 368-369 (1999). -Cowan R., Whittaker R.G. Hydrophobicity indices at ph 7.5 determined by HPLC. Peptide Research 3:75-80(1990). +Kawashima, S. and Kanehisa, M.; AAindex: amino acid index database. Nucleic Acids Res. 28, 374 (2000). +Kawashima, S., Pokarowski, P., Pokarowska, M., Kolinski, A., Katayama, T., and Kanehisa, M.; AAindex: amino acid index database, progress report 2008. Nucleic Acids Res. 36, D202-D205 (2008). %% ~~ possibly secondary sources and usages ~~ } \examples{ diff --git a/man/hmoment.Rd b/man/hmoment.Rd index a4880af..27295e6 100755 --- a/man/hmoment.Rd +++ b/man/hmoment.Rd @@ -5,7 +5,7 @@ %% ~~function to do ... ~~ } \description{ -This function compute the hmoment based on Eisenberg, D., Weiss, R. M., & Terwilliger, T. C. (1984). Hydriphobic moment is a quantitative measure of the amphiphilicity perpendicular to the axis of any periodic peptide structure, such as the a-helix or b-sheet. It can be calculated for an amino acid sequence of N residues and their associated hydrophobicities Hn. If the secuence length is < 11 AA, the window length is equal to the AA sequence length, if it is > 11, windows of 11 residues are evaluated} +This function compute the hmoment based on Eisenberg, D., Weiss, R. M., & Terwilliger, T. C. (1984). Hydriphobic moment is a quantitative measure of the amphiphilicity perpendicular to the axis of any periodic peptide structure, such as the a-helix or b-sheet. It can be calculated for an amino acid sequence of N residues and their associated hydrophobicities Hn. An 11 residues window is used as default.} \usage{ hmoment(seq,angle,window) @@ -18,6 +18,9 @@ hmoment(seq,angle,window) } \value{ The max hydrophobic moment (uH) as a numerical vector of length one} +\source{ +This function was written by an anonymous referee of the RJournal +} \references{ Eisenberg, D., Weiss, R. M., & Terwilliger, T. C. (1984). The hydrophobic moment detects periodicity in protein hydrophobicity. Proceedings of the National Academy of Sciences, 81(1), 140-144. } @@ -29,10 +32,10 @@ Eisenberg, D., Weiss, R. M., & Terwilliger, T. C. (1984). The hydrophobic moment # BETA-SHEET ANGLE=160 : 0.271 # ALPHA HELIX VALUE -hmoment(seq = "FLPVLAGLTPSIVPKLVCLLTKKC",angle = 100, window = 11) +hmoment(seq = "FLPVLAGLTPSIVPKLVCLLTKKC", angle = 100, window = 11) # [1] 0.5199226 # BETA SHEET VALUE -hmoment(seq = "FLPVLAGLTPSIVPKLVCLLTKKC",angle = 160, window = 11) +hmoment(seq = "FLPVLAGLTPSIVPKLVCLLTKKC", angle = 160, window = 11) # [1] 0.2705906 } \ No newline at end of file diff --git a/man/hydrophobicity.Rd b/man/hydrophobicity.Rd index cd25694..cd523ab 100644 --- a/man/hydrophobicity.Rd +++ b/man/hydrophobicity.Rd @@ -5,7 +5,7 @@ %% ~~function to do ... ~~ } \description{ -This function calculates the GRAVY hydrophobicity index of an amino acids sequence using one of the 24 scales availables on ExPASy "protscale" +This function calculates the GRAVY hydrophobicity index of an amino acids sequence using one of the 38 scales from different sources. %% ~~ A concise (1-5 lines) description of what the function does. ~~ } \usage{ @@ -14,58 +14,100 @@ hydrophobicity(seq,scale) %- maybe also 'usage' for other objects documented here. \arguments{ \item{seq}{amino acid sequence string in upper case} - \item{scale}{a character string specifying the hydophobicity scale to be used; must be one of \code{"KyteDoolittle"}, \code{"AbrahamLeo"}, \code{"BullBreese"},\code{"Guy"}, \code{"Miyazawa"}, \code{"Roseman"}, \code{"Wolfenden"}, \code{"Wilson"}, \code{"Cowan3.4"}, \code{"Aboderin"}, \code{"Sweet"}, \code{"Eisenberg"}, \code{"HoppWoods"}, \code{"Manavalan"}, \code{"BlackMould"}, \code{"Fauchere"}, \code{"Janin"}, \code{"Rao"}, \code{"Tanford"}, \code{"Cowan7.5"}, \code{"Chothia"} or \code{"Rose"}. + \item{scale}{a character string specifying the hydophobicity scale to be used; must be one of \code{"Aboderin"}, \code{"AbrahamLeo"}, \code{"Argos"}, \code{"BlackMould"}, \code{"BullBreese"}, \code{"Casari"}, \code{"Chothia"}, \code{"Cid"}, \code{"Cowan3.4"}, \code{"Cowan7.5"}, \code{"Eisenberg"}, \code{"Engelman"}, \code{"Fasman"}, \code{"Fauchere"}, \code{"Goldsack"}, \code{"Guy"}, \code{"HoppWoods"}, \code{"Janin"}, \code{"Jones"}, \code{"Juretic"}, \code{"Kidera"}, \code{"Kuhn"}, \code{"KyteDoolittle"}, \code{"Levitt"}, \code{"Manavalan"}, \code{"Miyazawa"}, \code{"Parker"}, \code{"Ponnuswamy"}, \code{"Prabhakaran"}, \code{"Rao"}, \code{"Rose"}, \code{"Roseman"}, \code{"Sweet"}, \code{"Tanford"}, \code{"Welling"}, \code{"Wilson"}, \code{"Wolfenden"} or \code{"Zimmerman"}. } } \source{ http://web.expasy.org/protscale/ + +http://www.genome.jp/aaindex/ } \references{ -Gasteiger, E., Hoogland, C., Gattiker, A., Wilkins, M. R., Appel, R. D., & Bairoch, A. (2005). Protein identification and analysis tools on the ExPASy server. In The proteomics protocols handbook (pp. 571-607). Humana Press. +Aboderin, A. A. (1971). An empirical hydrophobicity scale for alpha-amino-acids and some of its applications. International Journal of Biochemistry, 2(11), 537-544. -Eisenberg D., Schwarz E., Komarony M., Wall R. Normalized consensus hydrophobicity scale. J. Mol. Biol. 179:125-142(1984). +Abraham D.J., Leo A.J. Hydrophobicity (delta G1/2 cal). Proteins: Structure, Function and Genetics 2:130-152(1987). -Sweet R.M., Eisenberg D. Optimized matching hydrophobicity (OMH). J. Mol. Biol. 171:479-488(1983). +Argos, P., Rao, J. K., & Hargrave, P. A. (1982). Structural Prediction of Membrane-Bound Proteins. European Journal of Biochemistry, 128(2-3), 565-575. -Hopp T.P., Woods K.R. Hydrophilicity. Proc. Natl. Acad. Sci. U.S.A. 78:3824-3828(1981). +Black S.D., Mould D.R. Hydrophobicity of physiological L-alpha amino acids. Anal. Biochem. 193:72-82(1991). -Kyte J., Doolittle R.F. Hydropathicity. J. Mol. Biol. 157:105-132(1982). +Bull H.B., Breese K. Hydrophobicity (free energy of transfer to surface in kcal/mole). Arch. Biochem. Biophys. 161:665-670(1974). -Manavalan P., Ponnuswamy Average surrounding hydrophobicity. P.K. Nature 275:673-674(1978). +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. -Abraham D.J., Leo A.J. Hydrophobicity (delta G1/2 cal). Proteins: Structure, Function and Genetics 2:130-152(1987). +Chothia, C. (1976). The nature of the accessible and buried surfaces in proteins. Journal of molecular biology, 105(1), 1-12. -Black S.D., Mould D.R. Hydrophobicity of physiological L-alpha amino acids. Anal. Biochem. 193:72-82(1991). +Cid, H., Bunster, M., Canales, M., & Gazitua, F. (1992). Hydrophobicity and structural classes in proteins. Protein engineering, 5(5), 373-375. + +Cowan R., Whittaker R.G. Hydrophobicity indices at pH 3.4 determined by HPLC. Peptide Research 3:75-80(1990). -Bull H.B., Breese K. Hydrophobicity (free energy of transfer to surface in kcal/mole). Arch. Biochem. Biophys. 161:665-670(1974). +Cowan R., Whittaker R.G. Hydrophobicity indices at pH 7.5 determined by HPLC. Peptide Research 3:75-80(1990). + +Eisenberg D., Schwarz E., Komarony M., Wall R. Normalized consensus hydrophobicity scale. J. Mol. Biol. 179:125-142(1984). + +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. + +Fasman, G. D. (Ed.). (1989). Prediction of protein structure and the principles of protein conformation. Springer. Fauchere J.-L., Pliska V.E. Hydrophobicity scale (pi-r). Eur. J. Med. Chem. 18:369-375(1983). +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. + Guy H.R. Hydrophobicity scale based on free energy of transfer (kcal/mole). Biophys J. 47:61-70(1985). +Hopp T.P., Woods K.R. Hydrophilicity. Proc. Natl. Acad. Sci. U.S.A. 78:3824-3828(1981). + Janin J. Free energy of transfer from inside to outside of a globular protein. Nature 277:491-492(1979). +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. + +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. + +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. + +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. + +Kyte J., Doolittle R.F. Hydropathicity. J. Mol. Biol. 157:105-132(1982). + +Levitt, M. (1976). A simplified representation of protein conformations for rapid simulation of protein folding. Journal of molecular biology, 104(1), 59-107. + +Manavalan P., Ponnuswamy Average surrounding hydrophobicity. P.K. Nature 275:673-674(1978). + Miyazawa S., Jernigen R.L. Hydrophobicity scale (contact energy derived from 3D data). Macromolecules 18:534-552(1985). +Parker J.M.R., Guo D., Hodges R.S. Hydrophilicity scale derived from HPLC peptide retention times. Biochemistry 25:5425-5431(1986). + +Ponnuswamy, P. K. (1993). Hydrophobic charactesristics of folded proteins. Progress in biophysics and molecular biology, 59(1), 57-103. + +Prabhakaran, M. (1990). The distribution of physical, chemical and conformational properties in signal and nascent peptides. Biochem. J, 269, 691-696. + Rao M.J.K., Argos P. Membrane buried helix parameter. Biochim. Biophys. Acta 869:197-214(1986). +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) + Roseman M.A. Hydrophobicity scale (pi-r). J. Mol. Biol. 200:513-522(1988). -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). +Sweet R.M., Eisenberg D. Optimized matching hydrophobicity (OMH). J. Mol. Biol. 171:479-488(1983). -Wolfenden R.V., Andersson L., Cullis P.M., Southgate C.C.F. Hydration potential (kcal/mole) at 25C. Biochemistry 20:849-855(1981). +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). Welling G.W., Weijer W.J., Van der Zee R., Welling-Wester S. Antigenicity value X 10. FEBS Lett. 188:215-218(1985). 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). -Parker J.M.R., Guo D., Hodges R.S. Hydrophilicity scale derived from HPLC peptide retention times. Biochemistry 25:5425-5431(1986). +Wolfenden R.V., Andersson L., Cullis P.M., Southgate C.C.F. Hydration potential (kcal/mole) at 25C. Biochemistry 20:849-855(1981). -Cowan R., Whittaker R.G. Hydrophobicity indices at ph 3.4 determined by HPLC. Peptide Research 3:75-80(1990). +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. -Cowan R., Whittaker R.G. Hydrophobicity indices at ph 7.5 determined by HPLC. Peptide Research 3:75-80(1990). +Nakai, K., Kidera, A., and Kanehisa, M.; Cluster analysis of amino acid indices for prediction of protein structure and function. Protein Eng. 2, 93-100 (1988). -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) +Tomii, K. and Kanehisa, M.; Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins. Protein Eng. 9, 27-36 (1996). + +Kawashima, S., Ogata, H., and Kanehisa, M.; AAindex: amino acid index database. Nucleic Acids Res. 27, 368-369 (1999). + +Kawashima, S. and Kanehisa, M.; AAindex: amino acid index database. Nucleic Acids Res. 28, 374 (2000). + +Kawashima, S., Pokarowski, P., Pokarowska, M., Kolinski, A., Katayama, T., and Kanehisa, M.; AAindex: amino acid index database, progress report 2008. Nucleic Acids Res. 36, D202-D205 (2008). } \examples{ # COMPARED TO GRAVY Grand average of hydropathicity (GRAVY) ExPASy @@ -73,48 +115,80 @@ Rose G.D., Geselowitz A.R., Lesser G.J., Lee R.H., Zehfus M.H. Mean fractional a # SEQUENCE: QWGRRCCGWGPGRRYCVRWC # GRAVY: -0.950 -hydrophobicity("QWGRRCCGWGPGRRYCVRWC","KyteDoolittle") -# [1] -0.95 +hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Aboderin") +#[1] 3.84 hydrophobicity("QWGRRCCGWGPGRRYCVRWC","AbrahamLeo") -# [1] 0.09 +#[1] 0.092 +hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Argos") +#[1] 1.033 +hydrophobicity("QWGRRCCGWGPGRRYCVRWC","BlackMould") +#[1] 0.50125 hydrophobicity("QWGRRCCGWGPGRRYCVRWC","BullBreese") -# [1] 0.16 -hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Guy") -# [1] 0.19 -hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Miyazawa") -# [1] 5.74 -hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Roseman") -# [1] -0.5 -hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Wolfenden") -# [1] -6.31 -hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Wilson") -# [1] 3.16 +#[1] 0.1575 +hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Casari") +#[1] 0.38 +hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Chothia") +#[1] 0.262 +hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Cid") +#[1] 0.198 hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Cowan3.4") -# [1] 0.08 -hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Aboderin") -# [1] 3.84 -hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Sweet") -# [1] -0.11 +#[1] 0.0845 +hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Cowan7.5") +#[1] 0.0605 hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Eisenberg") -# [1] -0.33 -hydrophobicity("QWGRRCCGWGPGRRYCVRWC","HoppWoods") -# [1] -0.14 -hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Manavalan") -# [1] 13.04 -hydrophobicity("QWGRRCCGWGPGRRYCVRWC","BlackMould") -# [1] 0.5 +#[1] -0.3265 +hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Engelman") +#[1] 2.31 +hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Fasman") +#[1] -1.2905 hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Fauchere") -# [1] 0.53 +#[1] 0.527 +hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Goldsack") +#[1] 1.2245 +hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Guy") +#[1] 0.193 +hydrophobicity("QWGRRCCGWGPGRRYCVRWC","HoppWoods") +#[1] -0.14 hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Janin") -# [1] -0.1 +#[1] -0.105 +hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Jones") +#[1] 1.4675 +hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Juretic") +#[1] -1.106 +hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Kidera") +#[1] -0.0405 +hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Kuhn") +#[1] 0.9155 +hydrophobicity("QWGRRCCGWGPGRRYCVRWC","KyteDoolittle") +#[1] -0.95 +hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Levitt") +#[1] -0.21 +hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Manavalan") +#[1] 13.0445 +hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Miyazawa") +#[1] 5.739 +hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Parker") +#[1] 1.095 +hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Ponnuswamy") +#[1] 0.851 +hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Prabhakaran") +#[1] 9.67 hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Rao") -# [1] 0.81 -hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Tanford") -# [1] -0.29 -hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Cowan7.5") -# [1] 0.06 -hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Chothia") -# [1] 0.26 +#[1] 0.813 hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Rose") -# [1] 0.76 +#[1] 0.7575 +hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Roseman") +#[1] -0.495 +hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Sweet") +#[1] -0.1135 +hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Tanford") +#[1] -0.2905 +hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Welling") +#[1] -0.666 +hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Wilson") +#[1] 3.16 +hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Wolfenden") +#[1] -6.307 +hydrophobicity("QWGRRCCGWGPGRRYCVRWC","Zimmerman") +#[1] 0.943 } diff --git a/tests/doRUnit.R b/tests/doRUnit.R index dfb5e59..b852597 100644 --- a/tests/doRUnit.R +++ b/tests/doRUnit.R @@ -3,9 +3,9 @@ ## unit tests will not be done if RUnit is not available if(require("RUnit", quietly=TRUE)) { - + ## --- Setup --- - + pkg <- "Peptides" # <-- Change to package name! if(Sys.getenv("RCMDCHECK") == "FALSE") { ## Path to unit tests for standalone running under Makefile (not R CMD check) @@ -18,26 +18,26 @@ if(require("RUnit", quietly=TRUE)) { } cat("\nRunning unit tests\n") print(list(pkg=pkg, getwd=getwd(), pathToUnitTests=path)) - + library(package=pkg, character.only=TRUE) - + ## If desired, load the name space to allow testing of private functions ## if (is.element(pkg, loadedNamespaces())) ## attach(loadNamespace(pkg), name=paste("namespace", pkg, sep=":"), pos=3) ## ## or simply call PKG:::myPrivateFunction() in tests - + ## --- Testing --- - + ## Define tests testSuite <- defineTestSuite(name=paste(pkg, "unit testing"), dirs=path) ## Run tests <- runTestSuite(testSuite) - + ## Default report name pathReport <- file.path(path, "report") - + ## Report to stdout and text files cat("------------------- UNIT TEST SUMMARY ---------------------\n\n") printTextProtocol(tests, showDetails=FALSE) @@ -45,10 +45,10 @@ if(require("RUnit", quietly=TRUE)) { fileName=paste(pathReport, "Summary.txt", sep="")) printTextProtocol(tests, showDetails=TRUE, fileName=paste(pathReport, ".txt", sep="")) - + ## Report to HTML file printHTMLProtocol(tests, fileName=paste(pathReport, ".html", sep="")) - + ## Return stop() to cause R CMD check stop in case of ## - failures i.e. FALSE to unit tests or ## - errors i.e. R errors