NAME¶
theseus_align - quick-and-dirty way to superimpose proteins
SYNOPSIS¶
theseus_align [
theseus options] -f
pdbfile1.pdb
pdbfile2.pdb ...
OPTIONS¶
The options given to the script will be passed on to
theseus. For a
complete description, see the man page for
theseus (1).
DESCRIPTION¶
This manual page briefly documents briefly the script
theseus_align,
designed for a quick-and-dirty way to ML superposition proteins with different
sequences. It should work very well when the protein sequences are relatively
similar, although the ML method will still give much better results than
least-squares when the sequences are moderately divergent. Technically, this
procedure gives a structure-based superposition of a sequence-based alignment.
It
does not perform a structure-based alignment.
First, the script uses
theseus to create FASTA formatted sequence files
corresponding to the exact protein sequences found in the pdb files that you
supply.
Second, these sequences are aligned using the multiple sequence alignment
program of your choice. The script can easily be modified for CLUSTALW,
T_COFFEE, KALIGN, DIALIGN2, or MAFFT. Any multiple sequence alignment program
can be used, as long as it can generate clustal-formatted files. However, I
highly recommend Bob Edgar's MUSCLE program for both its speed and accuracy.
(For more info see
http://www.drive5.com/muscle/ .)
Third,
theseus performs a superposition of the structures using the
sequence alignment as a guide.
The installed version of
theseus_align uses
muscle (1) for doing
the multiple sequence alignment. If you wish to use one of the other programs
mentioned above, you'll have to copy the script to your own directory and edit
it.
SEE ALSO¶
theseus (1),
muscle (1),
clustalw (1),
t_coffee (1),
kalign (1),
dialign2 (1),
mafft (1). All of these
programs can be installed on Debian or Ubuntu systems using
apt-get
(8).
AUTHOR¶
theseus_align was written by Douglas L. Theobald, Department of
Biochemistry, Brandeis University.