Calculating Structures and Free Energies of Complex Molecules: Combining Molecular Mechanics and Continuum Models

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.

Keywords

Nucleic acidSolvationMolecular dynamicsMolecular mechanicsStatistical physicsImplicit solvationProtein foldingFolding (DSP implementation)MacromoleculeChemistryMoleculeComputational chemistryPhysicsChemical physicsQuantum mechanics

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Publication Info

Year: 2000
Type: article
Volume: 33
Issue: 12
Pages: 889-897
Citations: 4762
Access: Closed

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APA Style

                            
                                
                                    Peter A. Kollman, 
                                
                                    Irina Massova, 
                                
                                    Carolina Reyes
                                
                                et al.
                            
                            (2000). 
                            Calculating Structures and Free Energies of Complex Molecules:  Combining Molecular Mechanics and Continuum Models. 
                            Accounts of Chemical Research
                            , 33
                            (12)
                            , 889-897.
                            https://doi.org/10.1021/ar000033j
                        

Identifiers

DOI: 10.1021/ar000033j