DNA-binding of nickel (II), copper (II) and zinc (II) complexes: Structure–affinity relationships
Abstract Nickel (II), copper (II) and zinc (II) complexes with the same ligands normally display
analogous coordination geometry and binding mode toward DNA. However, although …
analogous coordination geometry and binding mode toward DNA. However, although …
Recent advances in small organic molecules as DNA intercalating agents: Synthesis, activity, and modeling
A Rescifina, C Zagni, MG Varrica, V Pistarà… - European journal of …, 2014 - Elsevier
The interaction of small molecules with DNA plays an essential role in many biological
processes. As DNA is often the target for majority of anticancer and antibiotic drugs, study …
processes. As DNA is often the target for majority of anticancer and antibiotic drugs, study …
Parmbsc1: a refined force field for DNA simulations
We present parmbsc1, a force field for DNA atomistic simulation, which has been
parameterized from high-level quantum mechanical data and tested for nearly 100 systems …
parameterized from high-level quantum mechanical data and tested for nearly 100 systems …
Routine microsecond molecular dynamics simulations with AMBER on GPUs. 2. Explicit solvent particle mesh Ewald
R Salomon-Ferrer, AW Gotz, D Poole… - Journal of chemical …, 2013 - ACS Publications
We present an implementation of explicit solvent all atom classical molecular dynamics (MD)
within the AMBER program package that runs entirely on CUDA-enabled GPUs. First …
within the AMBER program package that runs entirely on CUDA-enabled GPUs. First …
PTRAJ and CPPTRAJ: software for processing and analysis of molecular dynamics trajectory data
DR Roe, TE Cheatham III - Journal of chemical theory and …, 2013 - ACS Publications
We describe PTRAJ and its successor CPPTRAJ, two complementary, portable, and freely
available computer programs for the analysis and processing of time series of three …
available computer programs for the analysis and processing of time series of three …
Avoiding false positive conclusions in molecular simulation: the importance of replicas
Molecular simulations are a computational technique used to investigate the dynamics of
proteins and other molecules. The free energy landscape of these simulations is often …
proteins and other molecules. The free energy landscape of these simulations is often …
Optimization of the CHARMM additive force field for DNA: Improved treatment of the BI/BII conformational equilibrium
K Hart, N Foloppe, CM Baker, EJ Denning… - Journal of chemical …, 2012 - ACS Publications
The B-form of DNA can populate two different backbone conformations: BI and BII, defined
by the difference between the torsion angles ε and ζ (BI= ε–ζ< 0 and BII= ε–ζ> 0). BI is the …
by the difference between the torsion angles ε and ζ (BI= ε–ζ< 0 and BII= ε–ζ> 0). BI is the …
Introducing improved structural properties and salt dependence into a coarse-grained model of DNA
We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic
acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of …
acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of …
Sequence-dependent thermodynamics of a coarse-grained DNA model
originally designed to reproduce the properties of DNA molecules with average sequences.
The new parametrization introduces sequence-dependent stacking and base-pairing …
The new parametrization introduces sequence-dependent stacking and base-pairing …
Investigation of thermal properties of DNA structure with precise atomic arrangement via equilibrium and non-equilibrium molecular dynamics approaches
NA Jolfaei, NA Jolfaei, M Hekmatifar, A Piranfar… - Computer methods and …, 2020 - Elsevier
Abstract Background and Objective Thermal conductivity of Deoxyribonucleic acid
molecules is important for nanotechnology applications. Theoretical simulations based on …
molecules is important for nanotechnology applications. Theoretical simulations based on …