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.

MOTIVATION: Molecular dynamics (MD) simulations have become routine tools for the study of protein dynamics and function. Thanks to faster GPU-based algorithms, atomistic and coarse-grained simulations are being used to explore biological functions over the microsecond timescale, yielding terabytes of data spanning multiple trajectories, thereby extracting relevant protein conformations without losing important information is often challenging. RESULTS: We present MDSubSampler, a Python library and toolkit for a posteriori subsampling of data from multiple trajectories. This toolkit provides access to uniform, random, stratified, weighted sampling, and bootstrapping sampling methods. Sampling can be performed under the constraint of preserving the original distribution of relevant geometrical properties. Possible applications include simulations post-processing, noise reduction, and structures selection for ensemble docking. AVAILABILITY AND IMPLEMENTATION: MDSubSampler is freely available at https://github.com/alepandini/MDSubSampler, along with guidance on installation and tutorials on how it can be used.