Here is a short list of plugins related to protein structure analysis.

xPyder : a PyMOL plugin to analyze coupled residues and their networks in protein structures

https://pubmed.ncbi.nlm.nih.gov/22721491/

Azahar : a PyMOL plugin for construction, visualization and analysis of glycan molecules

https://pubmed.ncbi.nlm.nih.gov/27549814/

bcl::Cluster : A method for clustering biological molecules coupled with visualization in the Pymol Molecular Graphics System

https://pubmed.ncbi.nlm.nih.gov/27818847/

PyXlinkViewer : A flexible tool for visualization of protein chemical crosslinking data within the PyMOL molecular graphics system

https://pubmed.ncbi.nlm.nih.gov/32557917/

Templates for writing PyMOL scripts

https://pubmed.ncbi.nlm.nih.gov/33179363/

Automated protein motif generation in the structure-based protein function prediction tool ProMOL

https://pubmed.ncbi.nlm.nih.gov/26573864/

PyMod : sequence similarity searches, multiple sequence-structure alignments, and homology modeling within PyMOL

https://pubmed.ncbi.nlm.nih.gov/22536966/

Autodock/Vina plugin for PyMOL

https://mybiosoftware.com/autodockvina-plugin-pymol.html

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2881210/

PROVAT : a tool for Voronoi tessellation analysis of protein structures and complexes

https://pubmed.ncbi.nlm.nih.gov/15932902/