Enhancing sampling with free-energy calculations. (December 2022)

• Record Type: Journal Article
• Authors: Chen, Haochuan; Chipot, Christophe
• Is Part Of: Current opinion in structural biology. Volume 77(2022)
• Publication Date: 2022-12
• Subjects: Molecular biology -- Periodicals; 570
• DOI: 10.1016/j.sbi.2022.102497
• Languages: English
• ISSNs: 0959-440X

Abstract

Abstract: In recent years, considerable progress has been made to enhance sampling and help address biological questions, including, but not limited to conformational transitions in biomolecules and protein–ligand reversible binding, hitherto intractable by brute-force computer simulations. Many of these advances result from the development of a palette of methods aimed at exploring rare events through reliable free-energy calculations. The advent of new, often conceptually related methods has also rendered difficult the choice of the best suited option for a given problem. Here, we focus on geometrical transformations and algorithms designed to enhance sampling along adequately chosen progress variables, tracing their theoretical foundations, and showing how they are connected and can be blended together for improved performance. Graphical abstract: Image 1