shivChitinous / rad-gyres

calculating radii of gyration of proteins from .pdb files

rad-gyres

Check out protein structures here!

Visualizing centre of masses and radii of gyration for some proteins in the protein data bank (PDB).

read_process_PDB and radii_gyration.ipynb contain scripts for the following:

1. Downloading and parsing .pdb files
2. Plotting positions of skeletal atoms
3. Plotting all atoms
4. Plotting C and N termini
5. Calculating and plotting centre of mass
6. Calculating and plotting radius of gyration

References:

1. Lobanov, M.Y., Bogatyreva, N.S. & Galzitskaya, O.V. Radius of gyration as an indicator of protein structure compactness. Mol Biol 42, 623–628 (2008).
2. Rob Phillips, Jane Kondev, Julia Theriot, and Hernan G. Garcia. 1960. Physical Biology of the Cell. Second Edition.
3. Chaitanya Athale's Cellular Biophysics Course at IISER Pune

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