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 is easily 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. It is easy to install using either
precompiled binaries or by compiling from scratch:
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.
November, 2008