From 1faae5eef275bcf62615ac6061bb849b84832613 Mon Sep 17 00:00:00 2001 From: Daniel Camilo Osorio Date: Sun, 14 Dec 2014 20:00:36 -0500 Subject: [PATCH 1/8] Update 1.0.3 --- DESCRIPTION | 8 +- NEWS | 54 ++++++++++++ R/aindex.R | 2 +- R/charge.R | 2 +- R/hmoment.R | 15 ++-- R/hydrophobicity.R | 11 +-- R/membpos.R | 8 +- data/H.RData | Bin 4411 -> 5354 bytes data/pKscales.RData | Bin 3064 -> 3056 bytes inst/tests/runit.pI.R | 4 +- man/AAcomp.Rd | 18 ++-- man/Boman.Rd | 2 +- man/MW.Rd | 2 +- man/Peptides-package.Rd | 10 +-- man/aindex.Rd | 5 +- man/charge.Rd | 36 ++++---- man/h.Rd | 79 ++++++++++++++---- man/hmoment.Rd | 9 +- man/hydrophobicity.Rd | 180 ++++++++++++++++++++++++++++------------ 19 files changed, 310 insertions(+), 135 deletions(-) create mode 100644 NEWS diff --git a/DESCRIPTION b/DESCRIPTION index fb05cfd..07c53d6 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: 2014-12-12 +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..7ff7237 --- /dev/null +++ b/NEWS @@ -0,0 +1,54 @@ +NEWS +==== + +**Peptides v.1.0.3** +* membpos function bug fixed + +**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/charge.R b/R/charge.R index c2523e0..993a8cf 100755 --- a/R/charge.R +++ b/R/charge.R @@ -23,6 +23,6 @@ charge <- function(seq,pH=7,pKscale="EMBOSS"){ ccys <- aa["C"]* (-1 /(1+10^(-1*(pH-pKs["C"])))) ctyr <- aa["Y"]* (-1 /(1+10^(-1*(pH-pKs["Y"])))) # Compute the charge and return the value rounded to 3 decimals - charge <- round(as.numeric(carg + clys + chis + nterm + casp + cglu + ctyr + ccys + cterm),3) + charge <- as.numeric(carg + clys + chis + nterm + casp + cglu + ctyr + ccys + cterm) return(charge) } \ 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/data/H.RData b/data/H.RData index 769adee93928ad44f8cfd23e49618b3e1af283e3..d35e5c2b548c09c0fbac26710bcdfeb8f22400b4 100644 GIT binary patch literal 5354 zcmV?eBWl zcYU8{Egz?V@$v!k91cgEBOxZv5tr!AN{aXX5#va5 zclo!?Lr2`Z;Wlmk5Z+jEeZuR9j>*jnk0w9LEH6r!)V6u$lV?1N|3Q4W*aQ0fnr^q` 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z7$17Ab)bJR%Ae-3TA)09&_3?J1I$LqD*?ZY_aiW_S9X@(Ba+o0b4B$(2?ZL`i4mO` z(}^jan9~V@PR`Q^lgruPLYRDZ`JT;j@j?dB*Q5v8T# 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 } From d34c56bd778fba5c0ac68db21aa569de50be1433 Mon Sep 17 00:00:00 2001 From: Daniel Camilo Osorio Date: Sun, 14 Dec 2014 20:24:35 -0500 Subject: [PATCH 2/8] Update 1.0.3 --- DESCRIPTION | 2 +- NEWS | 2 +- README.md | 12 ++++++------ 3 files changed, 8 insertions(+), 8 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 07c53d6..eae97c7 100755 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: Peptides Version: 1.0.3 -Date: 2014-12-12 +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 diff --git a/NEWS b/NEWS index 7ff7237..63207bd 100644 --- a/NEWS +++ b/NEWS @@ -2,7 +2,7 @@ NEWS ==== **Peptides v.1.0.3** -* membpos function bug fixed +* A membpos function bug has been fixed. **Peptides v.1.0.2** diff --git a/README.md b/README.md index 65d5658..57e237f 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 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 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 | 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. 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"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, 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zT~qsX>`xR>G3lS)C7Gb=Yl0%_eFoM=GkE?^L%xyZpSN${&Y*+^-|Bq-3PphDZ#LHL Vl1`TB=wG6E^MCV=F%$P&004>861xBZ From 4706fd62b2246d95d88f9db83b5667b30539018e Mon Sep 17 00:00:00 2001 From: Daniel Camilo Osorio Date: Mon, 15 Dec 2014 10:09:18 -0500 Subject: [PATCH 6/8] Update 1.0.3 --- NEWS | 1 + 1 file changed, 1 insertion(+) diff --git a/NEWS b/NEWS index 63207bd..d317287 100644 --- a/NEWS +++ b/NEWS @@ -3,6 +3,7 @@ NEWS **Peptides v.1.0.3** * A membpos function bug has been fixed. +* The results now are not rounded. **Peptides v.1.0.2** From 5498e776574320e1d32956c55e79073952db8dca Mon Sep 17 00:00:00 2001 From: Daniel Camilo Osorio Date: Mon, 15 Dec 2014 10:11:35 -0500 Subject: [PATCH 7/8] Update 1.0.3 --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 57e237f..4d989c7 100755 --- a/README.md +++ b/README.md @@ -45,7 +45,7 @@ Available datasets ------------------- | Code | Description | |:----------- |:------------| -|H | 38 Hydrophobicity values for amino acids form ExPASy "protscale" | +|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 | From a5e13db8398ba0a8f1a356c5aeebf659124ec266 Mon Sep 17 00:00:00 2001 From: Daniel Camilo Osorio Date: Mon, 15 Dec 2014 10:12:18 -0500 Subject: [PATCH 8/8] Update 1.0.3 --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 4d989c7..7d12281 100755 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ Peptides ======== -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 GROMACS molecular dynamics package. +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 -------