Konnektor

Konnektor plans, modifies, and analyzes free energy calculation networks using graph theory to assist in drug discovery.

Key Features:

• Network Operations: The package contains functions for concatenation of networks, deletion of transformations, and clustering of molecules.
• Network Generation Framework: Konnektor provides a framework for combining network operation tools with existing network generation algorithms to enable the development of more complex methods for network generation.
• Visualization and Analysis Tools: The package contains tools for visualizing and analyzing network features.
• Network Layout Comparison: A comparison of various network layout features is carried out using toy data sets.

Scientific Applications:

• Alchemical Free Energy Campaign Planning: Konnektor enables systematic planning of free energy calculation networks where nodes represent molecules and edges represent possible transformations.
• Drug Discovery: Konnektor aids in the drug discovery process by enabling setup of free energy campaigns using complex graph manipulation methods.
• Network Performance Analysis: Application examples demonstrate how different networks perform from a graph theory perspective.

Methodology:

Konnektor uses graph theory to build networks with nodes representing molecules connected by edges representing possible transformations. The package implements complex graph manipulation methods including network concatenation, transformation deletion, and molecule clustering.