Structure-based drug design by denoising voxel grids

arXiv:2405.03961v1 Announce Type: new
Abstract: We present VoxBind, a new score-based generative model for 3D molecules conditioned on protein structures. Our approach represents molecules as 3D atomic density grids and leverages a 3D voxel-denoising network for learning and generation. We extend the neural empirical Bayes formalism (Saremi & Hyvarinen, 2019) to the conditional setting and generate structure-conditioned molecules with a two-step procedure: (i) sample noisy molecules from the Gaussian-smoothed conditional distribution with underdamped Langevin MCMC using the learned score function …

abstract arxiv bayes cs.lg denoising design drug design generative molecules network protein protein structures type voxel