Applications of enhanced sampling methods to biomolecular self-assembly: a review.

Journal: Journal of physics. Condensed matter : an Institute of Physics journal
Published Date:

Abstract

This review article discusses some common enhanced sampling methods in relation to the process of self-assembly of biomolecules. An introduction to self-assembly and its challenges is covered followed by a brief overview of the methods and analysis for replica-exchange molecular dynamics, umbrella sampling, metadynamics, and machine learning based techniques. Applications of select methods towards peptides, proteins, polymers, and nucleic acids are discussed. Finally, a short discussion of the future directions of some of these methods is provided.

Authors

  • Mason Hooten
    Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, United States of America.
  • Het Patel
    Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, United States of America.
  • Yiwei Shao
    Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, United States of America.
  • Rishabh Kumar Singh
    Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, United States of America.
  • Meenakshi Dutt
    Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, United States of America.