PyMol

DockingPie: DockingPie is a PyMOL plugin that offers a graphical interface for molecular and consensus docking analyses, integrating docking programs like Smina, Autodock Vina, RxDock, and ADFR.
iPBAVizu: iPBA: a tool for protein structure comparison using sequence alignment strategies
ProBis H2O plugin: ProBis H2O is a plugin for PyMOL that identifies conserved water sites in protein structures for drug design, supporting PyMOL version 2.3 and above on Linux and Windows.
ProBis H2O-MD plugin: ProBiS H2O MD Approach for Identification of Conserved Water Sites in Protein Structures for Drug Design
ProBis plugin: The ProBis plugin for PyMOL and UCSF Chimera enables users to detect protein binding sites, developed to work on Linux and tested in Windows environments, supporting PyMOL version 1.7.0.0 and UCSF Chimera version 1.11.

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