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Workflow for Structural Analysis of Single Point Mutations:
Workflow for Structural Analysis of Single Point Mutations:
Root-Mean-Squared Deviation (RMSD):
Root-Mean-Squared Deviation (RMSD):
Calculated by taking the square root of the difference between each atom's location in space (WT vs mutant) squared, divided by the number of total atoms. A common tool used for determining structural differences between similar proteins. Can be calculated in PyMol with the code "rms_cur WT_name, mutant_name".
Structural Analysis of Homo-tetramers:
Structural Analysis of Homo-tetramers:
Followed a similar workflow as point mutations shown above, except with tetramer structures built in AlphaFold colab.
To focus in on DNA Binding Domain (DBD), cut down full-length tetramer PDBs to only include sites 102-292 of the sequence.
DNA Docking:
DNA Docking:
Use the pyDockDNA program to model DNA docking
Receptor: Shortened DBD Tetramer
Ligand: CDKN1A DNA Structure
Example pyDockDNA input shown above.
Public Access Resources:
Public Access Resources:
UniProt: https://www.uniprot.org/uniprotkb/P04637/entry#sequences
ESMFold colab: https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/ESMFold.ipynb#scrollTo=CcyNpAvhTX6q
PyMol: https://pymol.org/edu/index.php
AlphaFold: https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb
web 3DNA 2.0: http://web.x3dna.org/custom/buildcomb
PyDockDNA: https://model3dbio.csic.es/pydockdna
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