An Evaluation of Unconditional 3D Molecular Generation Methods

Unconditional molecular generation is a stepping stone for conditional molecular generation, which is important in de novo drug design. Recent unconditional 3D molecular generation methods report saturated benchmarks, suggesting it is time to re-evaluate our benchmarks and compare the latest models. We assess five recent high-performing 3D molecular generation methods (EQGAT-diff, FlowMol, GCDM, GeoLDM, and SemlaFlow), in terms of both standard benchmarks and chemical and physical validity. Overall, the best method, SemlaFlow, has a success rate of 87 molecules without post-processing and 92.4