3DPhyloFold - a structure-based phylogeny tool

Published: 14-07-2020| Version 1 | DOI: 10.17632/kk3gkzdsbf.1
Gabriel Velez,
Young Joo Sun,
Dylan Parsons,
Alexander Bassuk,
Vinit Mahajan,
Jing Yang


3DPhyloFold aligns protein structural coordinates by their alpha carbon atoms to generate a root mean square deviation (RMSD) matrix. The matrix can then be analyzed by phylogenetic reconstruction software for high-throughput protein structural comparisons.


Steps to reproduce

Enclosed is python script for 3DPhyloFold.  1. Put the script under the same directory with the PDB files you would like to compare. 2. Open a terminal window and change the path to the PDB files folder.  3. Run the following command line: /Applications/PyMOL.app/Contents/MacOS/PyMOL -c 3DPhyloFold.py. Note - if using a MacOS system, you may need to point out the PyMOL directory for Python. You may want to change the highlighted part to your PyMOL directory.    4. You will then get a CSV file with the RMSD values under the same folder.