title: Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics.
abstract: Investigation of macromolecular structure and dynamics is fundamental to understanding how macromolecules carry out their functions in the cell. Significant advances have been made toward this end in silico, with a growing number of computational methods proposed yearly to study and simulate various aspects of macromolecular structure and dynamics. This review aims to provide an overview of recent advances, focusing primarily on methods proposed for exploring the structure space of macromolecules in isolation and in assemblies for the purpose of characterizing equilibrium structure and dynamics. In addition to surveying recent applications that showcase current capabilities of computational methods, this review highlights state-of-the-art algorithmic techniques proposed to overcome challenges posed in silico by the disparate spatial and time scales accessed by dynamic macromolecules. This review is not meant to be exhaustive, as such an endeavor is impossible, but rather aims to balance breadth and depth of strategies for modeling macromolecular structure and dynamics for a broad audience of novices and experts.
authors.affiliation: Department of Computer Science, George Mason University, Fairfax, Virginia, United States of America.
authors.forename: Tatiana
authors.identifier: 0000-0002-5605-0678
authors.initials: T
authors.lastname: Maximova
authors.affiliation: Department of Computer Science, George Mason University, Fairfax, Virginia, United States of America.
authors.forename: Ryan
authors.initials: R
authors.lastname: Moffatt
authors.affiliation: Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland, United States of America.
authors.forename: Buyong
authors.initials: B
authors.lastname: Ma
authors.affiliation: Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland, United States of America.|Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.
authors.forename: Ruth
authors.initials: R
authors.lastname: Nussinov
authors.affiliation: Department of Computer Science, George Mason University, Fairfax, Virginia, United States of America.|Department of Biongineering, George Mason University, Fairfax, Virginia, United States of America.|School of Systems Biology, George Mason University, Manassas, Virginia, United States of America.
authors.forename: Amarda
authors.identifier: 0000-0001-5230-4610
authors.initials: A
authors.lastname: Shehu
mesh_terms: D000465:Algorithms; D019295:Computational Biology; D003198:Computer Simulation; D046911:Macromolecular Substances / Q000737:chemistry*; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation / Q000706:statistics & numerical data*; D015394:Molecular Structure; D009010:Monte Carlo Method; D009696:Nucleic Acids / Q000737:chemistry; D017510:Protein Folding; D054730:Protein Interaction Domains and Motifs
chemical_list: D046911:Macromolecular Substances; D009696:Nucleic Acids