A Systematic Evaluation of Molecule Generation Models for De Novo Drug Design: From Benchmarks to Practical Insights

Abstract Molecule generation has emerged as a powerful computational tool for de novo drug design, enabling the exploration of the chemical space beyond the limits of conventional virtual screening. The field has progressed rapidly, driven by advances in molecular representations, generative architectures, and target-aware modeling strategies. However, existing reviews typically address specific model families or application scenarios in isolation rather than offering an integrated perspective on how these components collectively form a coherent generation workflow. In this review, we present a comprehensive evaluation of molecule generation models for de novo drug design, covering 82 methods across five deep generative frameworks, including recurrent neural network (RNN)- and transformer-based models, variational autoencoders (VAEs), generative adversarial networks (GANs), flow-based models, and diffusion models. We first summarize widely used benchmarks and molecular representations and then examine the methodological principles underlying both general and pocket-conditioned generation. A central contribution of this work is a systematic synthesis and comparative analysis of the reported performance across commonly used benchmarks and evaluation metrics. We also summarize representative experimentally validated cases. Looking ahead, we discuss future directions in standardized 3D data, interaction-aware generation, receptor flexibility, and multiobjective molecular design, with the aim of improving the reliability and experimental relevance of molecule generation. All collected benchmark resources, evaluation metrics, and model references are provided in a publicly accessible repository at https://github.com/JacklinGroup/molecule-generation-review.