Influence of divalent magnesium ion on DNA: molecular dynamics simulation studies

Structure and Dynamics of Double Helical DNA in Torsion Angle Hyperspace: A Molecular Mechanics Approach

(2012) Aditi Borkar et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Magnesium Ion–Water Coordination and Exchange in Biomolecular Simulations

(2012) Olof Allnér et al.   Journal of Chemical Theory and Computation

NMR Cross-Correlated Relaxation Rates Reveal Ion Coordination Sites in DNA

(2011) Radovan Fiala et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Recent developments and applications of the CHARMM force fields

(2011) Xiao Zhu et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Structural properties of polymeric DNA from molecular dynamics simulations

(2009) Sudipta Samanta et al.   JOURNAL OF CHEMICAL PHYSICS

A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA

(2009) Richard Lavery et al.   NUCLEIC ACIDS RESEARCH

Small local variations in B-form DNA lead to a large variety of global geometries which can accommodate most DNA-binding protein motifs

(2009) Arvind Marathe et al.   BMC STRUCTURAL BIOLOGY

Predicting Stability of DNA Duplexes in Solutions Containing Magnesium and Monovalent Cations

(2008) Richard Owczarzy et al.   BIOCHEMISTRY

Metal ions in biological catalysis: from enzyme databases to general principles

(2008) Claudia Andreini et al.   JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY

Molecular Dynamics Study of the Ribosomal A-Site

(2008) Julia Romanowska et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Towards a molecular dynamics consensus view of B-DNA flexibility

(2008) Alberto Pérez et al.   NUCLEIC ACIDS RESEARCH