JAMUN: Transferable Molecular Conformational Ensemble Generation with Walk-Jump Sampling

Conformational ensembles of protein structures are immensely important both to understanding protein function, and for drug discovery in novel modalities such as cryptic pockets. Current techniques for sampling ensembles are computationally inefficient, or do not transfer to systems outside their training data. We present walk-Jump Accelerated Molecular ensembles with Universal Noise (JAMUN), a step towards the goal of efficiently sampling the Boltzmann distribution of arbitrary proteins. By extending Walk-Jump Sampling to point clouds, JAMUN enables ensemble generation at orders of magnitude faster rates than traditional molecular dynamics or state-of-the-art ML methods. Further, JAMUN is able to predict the stable basins of small peptides that were not seen during training.

3D molecule generation by denoising voxel grids

We propose a new score-based approach to generate 3D molecules represented as atomic densities on regular grids. First, we train a denoising neural network that learns to map from a smooth distribution of noisy molecules to the distribution of real molecules. Then, we follow the neural empirical Bayes framework [Saremi and Hyvarinen, 2019] and generate molecules in two steps: (i) sample noisy density grids from a smooth distribution via underdamped Langevin Markov chain Monte Carlo, and (ii) recover the ``clean'' molecule by denoising the noisy grid with a single step. Our method, VoxMol, generates molecules in a fundamentally different way than the current state of the art (i.e., diffusion models applied to atom point clouds). It differs in terms of the data representation, the noise model, the network architecture and the generative modeling algorithm. VoxMol achieves comparable results to state of the art on unconditional 3D molecule generation while being simpler to train and faster to generate molecules.