MOTIVATION: Molecular Dynamics (MD) simulations are essential for investigating protein dynamics and function. Although significant advances have been made in integrating simulation techniques and machine learning, there are still challenges in selecting the most suitable data representation for learning. Graph embedding is a powerful computational method that automatically learns low-dimensional representations of nodes in a graph while preserving graph topology and node properties, thereby bridging graph structures and machine learning methods. Graph embeddings hold great potential for efficiently representing MD simulation data and studying protein dynamics. RESULTS: We present MDGraphEmb, a Python library built on MDAnalysis, specifically designed to convert protein MD simulation trajectories into graph-based representations and corresponding graph embeddings. This transformation enables the compression of high-dimensional, noisy trajectories from protein simulations into tabular formats suitable for machine learning. MDGraphEmb provides a framework that supports a range of graph embedding techniques and machine learning models, enabling the creation of workflows to analyse protein dynamics and identify important protein conformations. Graph embedding effectively captures and compresses structural information from protein MD simulation data, making it applicable to diverse downstream machine-learning classification tasks. We present an application for encoding and detecting important protein conformations from molecular dynamics simulations to classify functional states, using adenylate kinase (ADK) as the main case study. To assess the generalizability of the approach, two additional systems, Plantaricin E (PlnE) and HIV-1 protease are included as supplementary validation examples. A performance comparison of different graph embedding methods combined with machine learning models is also provided. AVAILABILITY AND IMPLEMENTATION: MDGraphEMB GitHub Repository: https://github.com/FerdoosHN/MDGraphEMB.

The self-organization of peptides into amyloidogenic oligomers is one of the key events for a wide range of molecular and degenerative diseases. Atomic-resolution characterization of the mechanisms responsible for the aggregation process and the resulting structures is thus a necessary step to improve our understanding of the determinants of these pathologies. To address this issue, we combine the accelerated sampling properties of replica exchange molecular dynamics simulations based on the OPEP coarse-grained potential with the atomic resolution description of interactions provided by all-atom MD simulations, and investigate the oligomerization process of the GNNQQNY for three system sizes: 3-mers, 12-mers and 20-mers. Results for our integrated simulations show a rich variety of structural arrangements for aggregates of all sizes. Elongated fibril-like structures can form transiently in the 20-mer case, but they are not stable and easily interconvert in more globular and disordered forms. Our extensive characterization of the intermediate structures and their physico-chemical determinants points to a high degree of polymorphism for the GNNQQNY sequence that can be reflected at the macroscopic scale. Detailed mechanisms and structures that underlie amyloid aggregation are also provided.