Concepedia

Unrestrained 5 ns molecular dynamics simulation of a cisplatin-DNA 1,2-GG adduct provides a rationale for the NMR features and reveals increased conformational flexibility at the platinum binding site

Miguel-Ángel Elizondo-Riojas, Jiřı́ Kozelka

Journal of Molecular Biology · 2001 · 47 citations · 46 references

Concepts

ChromatinNatural SciencesConformational FlexibilityMolecular BiologyDna ReplicationStructural BiologyNuclear OrganizationNmr FeaturesConformational StudyPlatinum Binding SiteDna ComputingMedicineMolecular DynamicsBiophysics

References

46

VMD: Visual molecular dynamics

William Humphrey, Andrew Dalke, Klaus Schulten · Journal of Molecular Graphics · 1996 · 64.1K citations

Engineering, Visual Molecular Dynamics, Molecular Biology +5

Particle mesh Ewald: An <i>N</i>⋅log(<i>N</i>) method for Ewald sums in large systems

Tom Darden, Darrin M. York, Lee G. Pedersen · The Journal of Chemical Physics · 1993 · 29.8K citations · Full text

Numerical Analysis, Engineering, Electrostatic Energies +18

A smooth particle mesh Ewald method

Ulrich Essmann, L. Perera, Max L. Berkowitz et al. · The Journal of Chemical Physics · 1995 · 22.3K citations

Numerical Analysis, Engineering, Particle Method +19

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

Jean-Paul Ryckaert, Giovanni Ciccotti, Herman J. C. Berendsen · Journal of Computational Physics · 1977 · 21.1K citations

Numerical Analysis, Cartesian Equations, Engineering +11

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

Peter A. Kollman, Irina Massova, Carolina Reyes et al. · Accounts of Chemical Research · 2000 · 4.8K citations