Data and code from: Decoding protein–membrane binding interfaces from surface-fingerprint-based geometric deep learning and molecular dynamics simulations

Predicting protein–membrane interactions is a formidable challenge due to the subtle physicochemical features that distinguish membrane-binding regions of a protein surface, as well as the scarcity of experimentally resolved membrane-bound protein conformations. Here, we present MaSIF-PMP, a geometric deep learning model that leverages molecular surface fingerprints to predict interfacial binding sites (IBSs) of peripheral membrane proteins (PMPs). MaSIF-PMP integrates geometric and chemical surface features to produce spatially resolved IBS predictions. Compared to existing models, MaSIF-PMP achieves superior performance for IBS classification, while feature ablation studies and transfer learning analyses reveal distinct determinants governing protein–membrane versus protein–protein interactions. We further show that molecular dynamics (MD) simulations can validate model predictions, refine IBS labels, and capture composition-dependent membrane binding patterns. These results establish..., , # README

Author: ByungUk Park\
README generated on: 10/21/2025

This archive (`data.tar.gz`) contains all data relevant to molecular dynamics (MD) simulations of peripheral membrane proteins (PMPs) with HMMM (Highly Mobile Membrane Mimetic) model systems, as described in the following work:

B. Park and R. C. Van Lehn. (2025). Decoding protein-membrane binding interfaces from surface-fingerprint-based geometric deep learning and molecular dynamics simulations. *bioRxiv*. [https://doi.org/10.1101/2025.10.14.682447](https://doi.org/10.1101/2025.10.14.682447).

The archive also includes scripts for running the simulations and generating MD-based membrane-binding interface labels. All simulations were performed using GROMACS 2021.5.

## File Types & Software Requirements

Among the simulation files, some (`.gro`, `.ndx`, `.top`, `.itp`, `.mdp` and `.xvg`) are plain text files that can be opened with standard text editors, while others (`.tpr`, `.xtc`) are binary files that require GROMACS ...,