THESEUS_ALIGN(1)

💖 THESEUS_ALIGN 💖

okay bestie, welcome to the theseus_align page — it's from the General Commands Manual, section 1, and it's literally the quick-and-dirty way to superimpose proteins. no cap. 🧚

✨ NAME ✨

theseus_align — quick-and-dirty way to superimpose proteins

🌸 SYNOPSIS 🌸

theseus_align [theseus options] -f pdbfile1.pdb pdbfile2.pdb ...

💅 OPTIONS 💅

• the options — whatever you hand the script gets passed straight on through to theseus. that's it, that's the whole list. if you want the full rundown, go read the man page for theseus (1). periodt.

🦋 DESCRIPTION 🦋

okay so this page is a lil brief documentation of the script theseus_align, and it's 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 — though honestly the ML method will still give you 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. important distinction, don't mix them up bestie.

here's the three-step slay:

1. 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.
2. 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/ .)
3. 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.

and that's the whole vibe, bestie — page THESEUS_ALIGN (1), November, 2008. go superimpose some proteins, you got this 💜🫶