2011/01/01 by Phineus R. L. Markwick, J. Andrew McCammon · 1 citation
Biochemistry, Genetics and Molecular Biology · Physics and Astronomy · Chemistry · #Protein Structure and Dynamics #Spectroscopy and Quantum Chemical Studies #DNA and Nucleic Acid Chemistry #Molecular dynamics #Allosteric regulation #Millisecond #A priori and a posteriori #Computer science #Representation (politics) #Biological system #Protein dynamics #Reaction coordinate #Metadynamics #Scale (ratio) #Chemistry #Computational chemistry #Physics #Biology
paper · doi:10.1039/c1cp22100k
openalex publication_date 2011/01/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/29
Many biologically important processes such as enzyme catalysis, signal transduction, ligand binding and allosteric regulation occur on the micro- to millisecond time-scale. Despite the sustained and rapid increase in available computational power and the development of efficient simulation algorithms, molecular dynamics (MD) simulations of proteins and bio-machines are generally limited to time-scales of tens to hundreds of nano-seconds. In this perspective article we present a comprehensive review of Accelerated Molecular Dynamics (AMD), an extended biased potential molecular dynamics approach that allows for the efficient study of bio-molecular systems up to time-scales several orders of magnitude greater than those accessible using standard classical MD methods, whilst still maintaining a fully atomistic representation of the system. Compared to many other approaches, AMD affords efficient enhanced conformational space sampling without any a priori understanding of the underlying free energy surface, nor does it require the specific prior definition of a reaction coordinate or a set of collective variables. Successful applications of the AMD method, including the study of slow time-scale functional dynamics in folded proteins and the conformational behavior of natively unstructured proteins are discussed and an outline of the different variants and extensions to the standard AMD approach is presented.