I haven't ever worked on protein visualization, yet I can suggest you try vedo https://vedo.embl.es/
Pymol and Chimera from UCSF both are leading 3D protein visualization programs and also have binding with python. However, suitability of the program will depend upon your problem statement which is not clear from your question.
Please elaborate your query if you need any specific answers.
Dear Kalungi Frank
These codes might be useful, have a look:
1. https://github.com/lmmentel/awesome-python-chemistry
2. https://github.com/hsiaoyi0504/awesome-cheminformatics
3. https://github.com/topics/protein-structure
4. https://github.com/topics/protein-structure?l=python
Kind Regards
Qamar Ul Islam
Dear Kalungi Frank
There are several python bases molecular visualization libraries/tools/widgets.
Following can be good choice if you want to embed on the fly molecular visualization inside some analysis script.
1. nglview: https://github.com/nglviewer/nglview. It comes as a widget for Jupiter notebook and can be used to visualize structure and trajectory
2. chemview: https://chemview.readthedocs.io/en/latest/
Structure prediction requires knowledge and intuition about the protein to be modeled. It depends if you have some knowledge about the similar proteins then you can go for homology modeling and Modeller: https://salilab.org/modeller/ is a python based good tool for it and free for academic use.
Ab-initio structure modeling is more difficult and may need to use some of them and evaluate which suites best your needs.
RasMol:
BioStructMap
https://medium.com/mlearning-ai/3d-sars-cov-2-protein-visualization-with-biopython-7c4f1955b1db
https://www.coursera.org/projects/3d-sars-cov-19-protein-visualization-with-biopython
and
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