2024/08/30 by Ao Ma, Huiyu Li, Ma, Ao +1 · 2 citations
Energy · Materials Science · #Biological Physics (physics.bio-ph) #Chemical Physics (physics.chem-ph) #FOS: Physical sciences #Global Energy and Sustainability Research #Machine Learning in Materials Science
paper · pdf · doi:10.48550/arxiv.2408.17086
openalex publication_date 2024/08/30 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
Reaction coordinates (RCs) are the few essential coordinates of a protein that control its functional processes, such as allostery, enzymatic reaction, and conformational change. They are critical for understanding protein function and provide optimal enhanced sampling of protein conformational changes and states. Since the pioneering works in the late 1990s, identifying the correct and objectively provable RCs has been a central topic in molecular biophysics and chemical physics. This review summarizes the major advances in identifying RCs over the past 25 years, focusing on methods aimed at finding RCs that meet the rigorous committor criterion, widely accepted as the true RCs. Importantly, the newly developed physics-based energy flow theory and generalized work functional method provide a general and rigorous approach for identifying true RCs, revealing their physical nature as the optimal channels of energy flow in biomolecules.