Dear Armando,
I have recently published a program which classifies/clusters protein
structures on the internal torsion angles, RoPE
(https://rope.hginn.co.uk). It is a GUI, in the form of a web
application and a preferable Mac executable (faster & multi-threaded).
I'm still working on setting up other binaries.
The scientific write-up of the tool is here, and also contains a written
tutorial for how to use the program:
https://onlinelibrary.wiley.com/doi/abs/10.1002/pro.4608
Additional instructions (particularly for loading your own PDB files or
metadata for analysis) can be found here:
https://rope.hginn.co.uk/index.php?page=dox
One serious advantage of using the internal torsion angles is that you
can skip the structural alignment (I would recommend using a different
program for this explicitly), and it describes the conformation of the
protein in the same parameter space as it naturally tends to flex. It
can also highlight the 'hinge' regions within your structure (i.e. the
backbone angles that vary the most). If you definitely want to cluster
on RMSD alone, do ask (it's been implemented for comparison purposes in
the paper, but is not the default option).
I'd recommend it to anyone who is looking to classify/understand
conformational changes across a range of related structures, regarding
both large and subtle modes of motion.
Best wishes
Helen
Dr Helen Ginn
Group leader, DESY
Hamburg Advanced Research Centre for Bioorganic Chemistry (HARBOR)
Luruper Chaussee 149
22607 Hamburg
########################################################################
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list
hosted by www.jiscmail.ac.uk, terms & conditions are available at
https://www.jiscmail.ac.uk/policyandsecurity/
