Calculating Structures and Free Energies of Complex Molecules: Combining Molecular Mechanics and Continuum Models
2000/10/04 by Peter A. Kollman, Irina Massova, Carolina Reyes +14 · 4,980 citations
Biochemistry, Genetics and Molecular Biology · Chemistry · #Chemical physics #Chemistry #Computational chemistry #DNA and Nucleic Acid Chemistry #Folding (DSP implementation) #Implicit solvation #Macromolecule #Molecular dynamics #Molecular mechanics #Molecule #Nucleic acid #Physics #Protein Structure and Dynamics #Protein folding #Quantum mechanics #RNA and protein synthesis mechanisms #Solvation #Statistical physics
paper · doi:10.1021/ar000033j
published in Accounts of Chemical Research 33(12), 889-897 (American Chemical Society)
openalex publication_date 2000/10/04 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/05
Abstract
A historical perspective on the application of molecular dynamics (MD) to biological macromolecules is presented. Recent developments combining state-of-the-art force fields with continuum solvation calculations have allowed us to reach the fourth era of MD applications in which one can often derive both accurate structure and accurate relative free energies from molecular dynamics trajectories. We illustrate such applications on nucleic acid duplexes, RNA hairpins, protein folding trajectories, and protein-ligand, protein-protein, and protein-nucleic acid interactions.
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