Predicting Molecular Conformation via Dynamic Graph Score MatchingDownload PDF

Published: 09 Nov 2021, Last Modified: 05 May 2023NeurIPS 2021 PosterReaders: Everyone
Keywords: Molecular conformation generation, score matching, generative model
Abstract: Predicting stable 3D conformations from 2D molecular graphs has been a long-standing challenge in computational chemistry. Recently, machine learning approaches have demonstrated very promising results compared to traditional experimental and physics-based simulation methods. These approaches mainly focus on modeling the local interactions between neighboring atoms on the molecular graphs and overlook the long-range interactions between non-bonded atoms. However, these non-bonded atoms may be proximal to each other in 3D space, and modeling their interactions is of crucial importance to accurately determine molecular conformations, especially for large molecules and multi-molecular complexes. In this paper, we propose a new approach called Dynamic Graph Score Matching (DGSM) for molecular conformation prediction, which models both the local and long-range interactions by dynamically constructing graph structures between atoms according to their spatial proximity during both training and inference. Specifically, the DGSM directly estimates the gradient fields of the logarithm density of atomic coordinates according to the dynamically constructed graphs using score matching methods. The whole framework can be efficiently trained in an end-to-end fashion. Experiments across multiple tasks show that the DGSM outperforms state-of-the-art baselines by a large margin, and it is capable of generating conformations for a broader range of systems such as proteins and multi-molecular complexes.
Code Of Conduct: I certify that all co-authors of this work have read and commit to adhering to the NeurIPS Statement on Ethics, Fairness, Inclusivity, and Code of Conduct.
Supplementary Material: pdf
TL;DR: we propose Dynamic Graph Score Matching (DGSM) for molecular conformation prediction, which models both the local and long-range interactions within molecules.
11 Replies

Loading