'proteinalign' is a R package that performs protein alignment using statistical shape analysis techiniques.
'proteinalign' depends on the Bioconductor's packages of 'Biostrings' and 'msa' which can be installed using
source('https://bioconductor.org/biocLite.R')
biocLite('Biostrings')
biocLite('msa')
Next, 'proteinalign' can be installed from the github repository using
install.packages('devtools')
devtools::install_github('thodorisgkolias/proteinalign')
and it can be loaded in R as usually with
library(proteinalign)
Load data
data1 <- LoadPDB('2gb1')
data2 <- LoadPDB('1ubq')
then putting it in a list using
data <- list(data1,data2)
Finally you can produce an alignment of these two protein molecules using
ProteinAlign(data, SP = 7, n.cores = 8)
GPL (>=2)