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BioMoleculePlot3D: visualizing proteins and other biomolecules

Posted 7 months ago
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Soutick Saha, Jan Mangaldan and Jason Biggs (2022).

BioMoleculePlot3D: visualizing proteins and other biomolecules. Wolfram Function Repository.

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POSTED BY: Soutick Saha
6 Replies

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POSTED BY: Moderation Team

8-22-22 Hi Soutick, Please tell us how these structures compare to any known 3D structures produced by published protein X-ray diffraction. Do you have statistical analysis as to how the structures reproduced here compare with X-ray diffraction data? In addition, do you have thermodynamics calculation to compare among similarly structured relationships?

Hi Paul,

Thanks a lot for the questions. These structures are generated using the coordinate files (mmCIF format) downloaded from protein databases (like RCSB PDB) which is derived from X-ray diffraction and NMR studies. The backbone corresponds to coordinates of alpha-Carbon atoms for amino acids and Phosphorus atoms for RNA.

The secondary structure (helices and sheet) information are also present in these files which helps us make these structures. Since these structures are generated using mmCIF files, they look very similar to structures in RCSB PDB.

We did not perform additional statistical or thermodynamic calculations.

Hope this answers your question.

Best, Soutick

POSTED BY: Soutick Saha

Great! Thanks!

@Soutick Saha these plots look fantastic! Great Job!

POSTED BY: Jason Biggs

Thanks a lot!

POSTED BY: Soutick Saha
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