GalaxyMemMD: an end-to-end Galaxy toolset for reproducible membrane embedding, molecular dynamics simulation, and analysis of membrane proteins

GalaxyMemMD is a comprehensive end-to-end framework for membrane protein research, developed as an automated, open-source solution within the Galaxy platform. This toolset addresses the critical challenge of accurately characterizing membrane proteins, which often prove difficult due to experimental constraints. While molecular dynamics (MD) simulations offer a powerful means of studying these proteins at the atomic level, executing simulations on a large scale can be prohibitively complex.

Existing tools focus primarily on system preparation for individual cases but lack a comprehensive, high-throughput pipeline that encompasses all stages—from membrane embedding to simulation and analysis—while supporting multiple membrane compositions and protein variants. Moreover, they often fail to integrate modern structure prediction and molecular docking frameworks.

GalaxyMemMD steps in to fill this gap by offering a single, reproducible pipeline that covers the entire process. By leveraging Galaxy's HPC-ready job scheduling capabilities, GalaxyMemMD can efficiently handle high-throughput parallel simulations across various membrane compositions and protein variants. Importantly, it supports AlphaFold-derived structural inputs and seamlessly incorporates downstream molecular docking workflows without the need for repeated manual setup.

The framework was validated across six structurally diverse membrane proteins, including four GPCRs, one ion channel, and one beta-barrel. These tests confirmed consistent system preparation and stable embeddings, with reproducible trajectory-level production workflows. GalaxyMemMD's performance matches that of established tools, demonstrating that it serves not only as a practical alternative but also as a valuable extension to the membrane protein simulation community.