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Parametric Protein Model from pdb file
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Protein model generated from pdb file, containing backbone and side chains. Example of single alpha helix protein GvpC
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Informacje o modelu
- Źródło
- Printables
- Kategoria
- Chemistry & Biology
- Licencja
- Creative Commons — Attribution — Noncommercial — Share Alike
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ColabProteinPrint v0.1
Google Colab to convert an atomic model of a protein into a series of 3D printable stl files.
https://github.com/stefanhuber1993/ColabProteinPrint
Features
- PDB input file is split in backbone and amino acid parts
- Amino acids are oriented in a standardized way for 3D printing
- Residue number is printed on the C-alpha hydrogen atom
- Phi and psi angles are encoded directly into the printed model as little notches.
- Trans and cis peptide bonds included
- Parametric model with customizable bond thicknesses and tolerances
Limitations
- Support for proline is implemented but not yet properly tested
Example
- The included print files are for a single 33 amino acid repeat of the protein GvpC
- https://www.uniprot.org/uniprotkb/P09413/entry
Further details
- Further details about the model can be found in my PhD thesis “Imaging Life at the Molecular Scale using Electrons, 2024” https://repository.tudelft.nl/record/uuid:9673dae3-5a3d-4544-a48e-dcd088c72625