Tracing compound pathways using chemical space networks

Visualizing chemical space networks with RDKit and NetworkX

This article demonstrates how to create Chemical Space Networks (CSNs) using a Python RDKit and NetworkX workflow. CSNs are a type of network visualization that depict compounds as nodes connected by edges, defined as a pairwise relationship such as a 2D fingerprint similarity value. A step by step approach is presented for creating two different CSNs in this manuscript, one based on RDKit 2D fingerprint Tanimoto similarity values, and another based on maximum common substructure similarity values. Several different CSN visualization features are included in the tutorial including methods to represent nodes with color based on bioactivity attribute value, edges with different line styles based on similarity value, as well as replacing the circle nodes with 2D structure depictions. Finally, some common network property and analysis calculations are presented including the clustering coefficient, degree assortativity, and modularity. All code is provided in the form of Jupyter Notebooks and is available on GitHub with a permissive BSD-3 open-source license: https://github.com/vfscalfani/CSN_tutorial.

Towards Predictive Synthesis of Inorganic Materials Using Network Science

Accelerating materials discovery is the cornerstone of modern technological competitiveness. Yet, the inorganic synthesis of new compounds is often an important bottleneck in this quest. Well-established quantum chemistry and experimental synthesis methods combined with consolidated network science approaches might provide revolutionary knowledge to tackle this challenge. Recent pioneering studies in this direction have shown that the topological analysis of material networks hold great potential to effectively explore the synthesizability of inorganic compounds. In this Perspective we discuss the most exciting work in this area, in particular emerging new physicochemical insights and general concepts on how network science can significantly help reduce the timescales required to discover new materials and find synthetic routes for their fabrication. We also provide a perspective on outstanding problems, challenges and open questions.