Quick-and-dirty way to superimpose proteins
theseus_align [theseus options] -f pdbfile1.pdb pdbfile2.pdb ...
The options given to the script will be passed on to theseus. For a complete description, see the man page for theseus (1).
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.
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).
theseus_align was written by Douglas L. Theobald, Department of Biochemistry, Brandeis University.