Ramachandran plotting tool
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Updated
Oct 25, 2026 - Python
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ramachandran
Here are 7 public repositories matching this topic...
Program to plot a Ramachandran plot of all dihedral angles from a given PDB file. Background is empirically generated from the peptides in the Top8000 PDB data set.
modern structural-biology pdb protein-data-bank protein-structure plot mmcif peptides dihedral-angles ramachandran-plot ramachandran
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Feb 25, 2025 - Jupyter Notebook
Compact sequence-only neural propagator for protein torsion dynamics. 2.39x lower JSD than Microsoft Timewarp at 3000x fewer parameters. pip install alphadynamics.
python molecular-dynamics pytorch reservoir-computing protein-dynamics ramachandran neural-ode torsion-angles apache-2 claude-code-plugin phase-oscillators ml-for-biology
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May 9, 2026 - Python
R code & Python code for creating Ramachandran Plot (MAT Feature)
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Jun 7, 2017 - R
A simple script to generate Ramachandran plot from Pymol.
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Nov 7, 2021 - Python
Generate realistic PDB files with mixed secondary structures for testing, education and bioinformatics tool development. Jupyter Notebook tutorials are available to visualize the concepts..
bioinformatics simulation structural-biology protein-data-bank protein-structure molecular-dynamics protein scientific-computing secondary-structure biophysics nmr-spectroscopy structural-bioinformatics ramachandran molecular-modeling peptide-sequences computational-biophysics science-education computational-structural-biology nmr-tools
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Jun 29, 2026 - Python
Validate a real protein structure with a Ramachandran plot of backbone phi/psi dihedral angles against allowed regions.
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Aug 12, 2026 - Python
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