Generalized Implicit Neural Representations for Dynamic Molecular Surface Modeling

Abstract Molecular dynamics (MD) has long been the de facto choice for simulating intricate physical systems from first principles. Recent efforts utilize the implicit neural representation (INR) to directly learn surface point clouds' signed distance function (SDF) with promising outcomes. However, INR's temporal generalization to unexplored molecular systems remains limited, which poses a significant barrier to applying INR to a broader range of real-world scenarios. This study introduces MoE-DSR, an enhanced version of dynamic surface representations (DSR) that effectively integrates the mixture-of-experts (MoE) strategy. Specifically, the router employs a novel geometric surface cloud network to extract the structural information from the initial static protein conformation as the prior knowledge. Meanwhile, experts compromising a team of equivariant implicit neural networks (E-INNs), each responsible for distinct protein families, ensure precise SDF estimation across varied protein data landscapes. We showcase the ability of MoE-DSR to model dynamic protein surface shapes using ensembles from ATLAS, the largest available protein MD simulations database. Extensive experiments validate its effectiveness in analyzing complex molecular systems across continuous space and time domains.