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

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

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

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

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

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

Code | Function |
---|---|

aaList | Return a vector with the 20 standard aminoacids in upper case |

aaComp | Compute the amino-acid composition of a protein sequence |

aaDescriptors | Compute 66 descriptors for each amino acid of a protein sequence |

aIndex | Compute the aliphatic index of a protein sequence |

autoCorrelation | Compute the auto-correlation index of a protein sequence |

autoCovariance | Compute the auto-covariance index of a protein sequence |

blosumIndices | Compute the BLOSUM62 derived indices of a protein sequence |

boman | Compute the Boman (Potential Protein Interaction) index |

charge | Compute the theoretical net charge of a protein sequence |

crossCovariance | Compute the cross-covariance index of a protein sequence |

crucianiProperties | Compute the Cruciani properties of a protein sequence |

fasgaiVectors | Compute the FASGAI vectors of a protein sequence |

hmoment | Compute the hydrophobic moment of a protein sequence |

hydrophobicity | Compute the hydrophobicity index of a protein sequence |

instaIndex | Compute the instability index of a protein sequence |

kideraFactors | Compute the Kidera factors of a protein sequence |

lengthpep | Compute the aminoacid length of a protein sequence |

massShift | Compute the mass difference of a protein sequence labelled with stable isotope. |

membpos | Compute theoretically the class of a protein sequence |

mswhimScores | Compute the MS-WHIM scores of a protein sequence |

mw | Compute the molecular weight of a protein sequence |

mz | Compute the mass over charge (m/z) of a protein sequence |

pI | Compute the isoelectic point (pI) of a protein sequence |

plotXVG | Plot time series from GROMACS XVG files |

protFP | Compute the protFP descriptors of a protein sequence |

readXVG | Read XVG files from GROMACS molecular dynamics package |

stScales | Compute the ST-scales of a protein sequence |

tScales | Compute the T-scales of a protein sequence |

vhseScales | Compute the VHSE-scales of a protein sequence |

zScales | Compute the Z-scales of a protein sequence |

Code | Description |
---|---|

AAdata | Properties, scales and indices for the 20 naturally occurring amino acids from various sources |

pepdata | A data frame with 21 physicochemical properties and indices from 100 amino-acid sequences (50 antimicrobial and 50 non antimicrobial) |

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