mustang. bio3d 2.3-0

Usage

mustang(files, exefile="mustang", outfile="aln.mustang.fa", cleanpdb=FALSE, cleandir="mustangpdbs", verbose=TRUE)

Arguments

files: a character vector of PDB file names.
exefile: file path to the ‘MUSTANG’ program on your system (i.e. how is ‘MUSTANG’ invoked).
outfile: name of ‘FASTA’ output file to which alignment should be written.
cleanpdb: logical, if TRUE iterate over the PDB files and map non-standard residues to standard residues (e.g. SEP->SER..) to produce ‘clean’ PDB files.
cleandir: character string specifying the directory in which the ‘clean’ PDB files should be written.
verbose: logical, if TRUE ‘MUSTANG’ warning and error messages are printed.

Description

Create a multiple sequence alignment from a bunch of PDB files.

Details

Structure-based sequence alignment with ‘MUSTANG’ attempts to arrange and align the sequences of proteins based on their 3D structure.

This function calls the ‘MUSTANG’ program, to perform a multiple structure alignment, which MUST BE INSTALLED on your system and in the search path for executables.

Note that non-standard residues are mapped to “Z” in MUSTANG. As a workaround the bio3d ‘mustang’ function will attempt to map any non-standard residues to standard residues (e.g. SEP->SER, etc). To avoid this behaviour use ‘cleanpdb=FALSE’.

Value

ali: an alignment character matrix with a row per sequence and a column per equivalent aminoacid.
ids: sequence names as identifers.

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.

‘MUSTANG’ is the work of Konagurthu et al: Konagurthu, A.S. et al. (2006) Proteins 64(3):559--74.

More details of the ‘MUSTANG’ algorithm, along with download and installation instructions can be obtained from: http://www.csse.monash.edu.au/~karun/Site/mustang.html.

Note

A system call is made to the ‘MUSTANG’ program, which must be installed on your system and in the search path for executables.

Examples

## Fetch PDB files and split to chain A only PDB files
ids <- c("1a70_A", "1czp_A", "1frd_A")
files <- get.pdb(ids, split = TRUE, path = tempdir())


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##-- Or, read a folder/directory of existing PDB files
#pdb.path <- "my_dir_of_pdbs"
#files  <- list.files(path=pdb.path ,
#                     pattern=".pdb",
#                     full.names=TRUE)

##-- Align these PDB sequences
aln <- mustang(files)

Running command
 mustang -f /tmp/RtmpTDihxb/filecfdb57737ba6 -o /tmp/RtmpTDihxb/filecfdb453ee916 -F fasta 


##-- Read Aligned PDBs storing coordinate data
pdbs <- read.fasta.pdb(aln) 

pdb/seq: 1   name: /tmp/RtmpTDihxb/split_chain/1a70_A.pdb 
pdb/seq: 2   name: /tmp/RtmpTDihxb/split_chain/1czp_A.pdb 
   PDB has ALT records, taking A only, rm.alt=TRUE
pdb/seq: 3   name: /tmp/RtmpTDihxb/split_chain/1frd_A.pdb

Author

Lars Skjaerven

Structure-based Sequence Alignment with MUSTANG