FE-ToolKit: A Versatile Software Suite for Analysis of High-Dimensional Free Energy Surfaces and Alchemical Free Energy Networks
Year: 2025
Type: article
Abstract: Free energy simulations play a pivotal role in diverse biological applications, including enzyme design, drug discovery, and biomolecular engineering. The characterization of high-dimensional free energy surfaces underlying complex enzymatic mechanisms necessitates extensive sampling through umbrella sampling or string method simulations. Accurate ranking of target-binding free energies across large ligand libraries relies on comprehensive alchemical free energy calculations organized into thermodynamic networks. The predictive accuracy of these methods hinges on robust, scalable tools for networkwide data analysis and extraction of physical properties from heterogeneous simulation data. Here, we introduce FE-ToolKit, a versatile software suite for the automated analysis of free energy surfaces, minimum free energy paths, and alchemical free energy networks (thermodynamic graphs).
Institution: Rutgers, The State University of New Jersey
Language: English
Subfield: Drug Discovery
Domain: Life Sciences
Open Access status: hybrid
Estimated APC paid: $4,500
Awards: Collaborative Research: Frameworks: Interoperable High-Performance Classical, Machine Learning and Quantum Free Energy Methods in AMBER, Track 4: Advanced CI Coordination Ecosystem: Monitoring and Measurement Services, Track 1: ACCESS Resource Allocations Marketplace and Platform Services (RAMPS), ACO: An Open CI Ecosystem to Advance Scientific Discovery (OpenCI), Track 3: COre National Ecosystem for CyberinfrasTructure (CONECT), Track 2: Customized Multi-tier Assistance, Training, and Computational Help (MATCH) for End User ACCESS to CI, Computational Enzymology to Study Diverse Catalytic Strategies of RNA, Next-generation alchemical free energy methods and quantum/machine-learning models for drug discovery
OpenAlex ID: W4410567690