2023/07/18 by Diego E. Kleiman, Kleiman, Diego E., Hassan Nadeem +3
Biochemistry, Genetics and Molecular Biology · Engineering · Physics and Astronomy · #Biomolecules (q-bio.BM) #FOS: Biological sciences #Microfluidic and Capillary Electrophoresis Applications #NMR spectroscopy and applications #Protein Structure and Dynamics
paper · pdf · doi:10.48550/arxiv.2307.09664
openalex publication_date 2023/07/18 · openalex created_date 2023/07/21 · openalex updated_date 2026/07/28
Molecular Dynamics (MD) simulations are fundamental computational tools for the study of proteins and their free energy landscapes. However, sampling protein conformational changes through MD simulations is challenging due to the relatively long timescales of these processes. Many enhanced sampling approaches have emerged to tackle this problem, including biased and path-sampling methods. In this perspective, we focus on adaptive sampling algorithms. These techniques differ from other approaches because the thermodynamic ensemble is preserved and the sampling is enhanced solely by restarting MD trajectories at particularly chosen seeds, rather than introducing biasing forces. We begin our treatment with an overview of theoretically transparent methods where we discuss principles and guidelines for adaptive sampling. Then, we present a brief summary of select methods that have been applied to realistic systems in the past. Finally, we discuss recent advances in adaptive sampling methodology powered by machine learning techniques as well as their shortcomings.