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Deep learning framework for molecular docking extending AutoDock Vina with convolutional neural network scoring functions, achieving superior virtual screening enrichment and pose prediction across diverse target classes; widely adopted in pharmaceutical structure-based drug design (J. Cheminformatics, 915+ stars, actively maintained)

A graph-based molecule modeling and chemoinformatics analysis toolkit fully implemented in Julia

Diffusion-based generative model for inorganic materials design, steering generation by chemistry, symmetry, bulk modulus, band gap, or magnetic properties, 2× more likely to produce stable novel structures than prior methods, experimentally validated with synthesized TaCr₂O₆ (Microsoft, Nature 2025)

Another list focuses on Python stuff related to Chemistry.

Therapeutics Data Commons: 66 AI-ready datasets across 22 drug discovery tasks with 29 leaderboards, covering target identification, molecular generation, ADMET prediction, and clinical trial outcomes (Harvard MIMS, NeurIPS 2021/2024)