May 8, 2024, 4:41 a.m. | Pedro O. Pinheiro, Arian Jamasb, Omar Mahmood, Vishnu Sresht, Saeed Saremi

cs.LG updates on arXiv.org arxiv.org

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

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