Dear Van Dung Pham ,

A good starting point might be:

Westhead, D. R., Slidel, T. W., Flores, T. P., & Thornton, J. M. (1999). Protein structural topology: Automated analysis and diagrammatic representation. Protein Science, 8(4), 897-904.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2144300/

Nice software program is TopDraw see for more info the following discussion:

https://www.researchgate.net/post/Does_anyone_have_any_link_for_downloading_TopDraw_topology_diagram_maker

PS. Very nice paper I can recommend:

Almeida, J. G., Preto, A. J., Koukos, P. I., Bonvin, A. M., & Moreira, I. S. (2017). Membrane proteins structures: A review on computational modeling tools. Biochimica et Biophysica Acta (BBA)-Biomembranes, 1859(10), 2021-2039. Best regards.

Dear Rob Keller ,

Thanks for your sharing. I appreciate that.

Hi Van,

Pro-origami is pretty simple to use and web-based, it is relatively old but still reliable. You can feed him with a PDB file if you have it and it will do everything.

http://munk.csse.unimelb.edu.au/pro-origami/

Alternatively i know that the EBI has a service that allows you to load your PDB file on PDBsum and visualize a lot of info on your protein. I never used this actually.

https://www.ebi.ac.uk/thornton-srv/databases/pdbsum/Generate.html

Also, you should be able to generate 3D (not 2D I think) topological structures with most protein visualizers, such as the "classic" PyMol.