EnsembleFlex: Protein structure ensemble analysis made easy

Abstract

Proteins exhibit conformational dynamics that underpin function and inform drug design. EnsembleFlex is a computational suite to extract, quantify, and visualize conformational heterogeneity from experimentally determined structure ensembles, thereby enabling both computational and experimental scientists to gain actionable insights into protein dynamics, ligand interactions, and drug-design applications. It performs dual-scale flexibility analysis (backbone and side-chain) via optimized superposition, dimension reduction (principal-component analysis [PCA] and uniform manifold approximation and projection [UMAP]), clustering, automated binding-site frequency mapping, and conserved water detection. Accessible through a no-code graphical interface or scriptable pipelines, EnsembleFlex accepts heterogeneous PDB sets (X-ray, NMR, and cryoelectron microscopy [cryo-EM]) and optionally integrates elastic network-model predictions (anisotropic network model [ANM]/Gaussian network model [GNM]) to complement experimental data. Case studies—including adenylate kinase, hexokinase-1, interleukin-1β (IL-1β) fragment screens, and SARS-CoV-2 main protease ensembles—demonstrate its scalability and utility for high-throughput structural analysis.