Read the Distill articles "Understanding Convolutions on Graphs"

Read the Distill articles "A Gentle Introduction ot Graph Neural Networks"

Petar Veličković's nice YouTube video titled "Theoretical Foundations of Graph Neural Networks"

"A Hitchhiker's Guide to Geometric GNNs for 3D Atomic Systems" is a widely red resource. 

Try out the CGCNN model and read the corresponding paper titled Crystal Graph Convolutional Neural Netowrks paper. 

Some openly accessible datasets: awesome-matchem-datsets

PyTorch Geometric for graph-based deep learning (tuotrials)

Great resource to learn PyTorch Geomeric is the Github page of Antonio Longa (PyTorchGeometricTutorial)

Standford CS224W: Machine Learning with Graphs (capstone projects)