New Effective Method for Quantitative Analysis of Diffusion Jumps, Applied in Molecular Dynamics Simulations of Small Molecules Dispersed in Short Chain Systems

2007 ◽  
Vol 111 (49) ◽  
pp. 13683-13693 ◽  
Author(s):  
Theophanes E. Raptis ◽  
Vasilios E. Raptis ◽  
Jannis Samios
Keyword(s):  
Molecular Dynamics ◽  
Quantitative Analysis ◽  
Small Molecules ◽  
Molecular Dynamics Simulations ◽  
Short Chain ◽  
Dynamics Simulations

Parameterization of prototype organic small molecules suitable for OPVs and molecular dynamics simulations: the BTT and BPT cases

2019 ◽  
Vol 25 (5) ◽  
Author(s):  
Karl M. García-Ruiz ◽  
Andrés F. Marmolejo-Valencia ◽  
Augusto González-Navejas ◽  
Laura Dominguez ◽  
Carlos Amador-Bedolla
Keyword(s):  
Molecular Dynamics ◽  
Small Molecules ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulations

scholarly journals Membrane permeability of small molecules from unbiased molecular dynamics simulations

2020 ◽  
Vol 153 (12) ◽  
pp. 124107 ◽  
Author(s):  
Andreas Krämer ◽  
An Ghysels ◽  
Eric Wang ◽  
Richard M. Venable ◽  
Jeffery B. Klauda ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Small Molecules ◽  
Molecular Dynamics Simulations ◽  
Membrane Permeability ◽  
Dynamics Simulations

scholarly journals Enhanced sampling molecular dynamics simulations correctly predict the diverse activities of a series of stiff-stilbene G-quadruplex DNA ligands

2021 ◽  
Author(s):  
Michael P. O'Hagan ◽  
Susanta Haldar ◽  
Juan C. Morales ◽  
Adrian J. Mulholland ◽  
M. Carmen Galan
Keyword(s):  
Molecular Dynamics ◽  
Small Molecules ◽  
Molecular Dynamics Simulations ◽  
Solution Phase ◽  
Enhanced Sampling ◽  
Quadruplex Dna ◽  
G Quadruplex ◽  
Dynamics Simulations

Enhanced sampling molecular dynamics simulations and solution-phase experiments come together to demonstrate the diverse effects of G4-interactive small molecules.

scholarly journals Flexible Fitting of Small Molecules into Electron Microscopy Maps Using Molecular Dynamics Simulations with Neural Network Potentials

2020 ◽  
Vol 60 (5) ◽  
pp. 2591-2604 ◽  
Author(s):  
John W. Vant ◽  
Shae-Lynn J. Lahey ◽  
Kalyanashis Jana ◽  
Mrinal Shekhar ◽  
Daipayan Sarkar ◽  
...  
Keyword(s):  
Neural Network ◽  
Electron Microscopy ◽  
Molecular Dynamics ◽  
Small Molecules ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulations

scholarly journals Learning to Model G-Quadruplexes: Current Methods and Perspectives

2021 ◽  
Vol 50 (1) ◽  
Author(s):  
Iker Ortiz de Luzuriaga ◽  
Xabier Lopez ◽  
Adrià Gil3
Keyword(s):  
Molecular Dynamics ◽  
Small Molecules ◽  
Molecular Dynamics Simulations ◽  
Density Functional ◽  
Experimental Studies ◽  
Annual Review ◽  
Publication Date ◽  
Square Planar ◽  
Explicit Simulation ◽  
Dynamics Simulations

G-quadruplexes have raised considerable interest during the past years for the development of therapies against cancer. These noncanonical structures of DNA may be found in telomeres and/or oncogene promoters, and it has been observed that the stabilization of such G-quadruplexes may disturb tumor cell growth. Nevertheless, the mechanisms leading to folding and stabilization of these G-quadruplexes are still not well established, and they are the focus of much current work in this field. In seminal works, stabilization was observed to be produced by cations. However, subsequent studies showed that different kinds of small molecules, from planar and nonplanar organic molecules to square-planar and octahedral metal complexes, may also lead to the stabilization of G-quadruplexes. Thus, the comprehension and rationalization of the interaction of these small molecules with G-quadruplexes are also important topics of current interest in medical applications. To shed light on the questions arising from the literature on the formation of G-quadruplexes, their stabilization, and their interaction with small molecules, synergies between experimental studies and computational works are needed. In this review, we mainly focus on in silico approaches and provide a broad compilation of different leading studies carried out to date by different computational methods. We divide these methods into two main categories: ( a) classical methods, which allow for long-timescale molecular dynamics simulations and the corresponding analysis of dynamical information, and ( b) quantum methods (semiempirical, quantum mechanics/molecular mechanics, and density functional theory methods), which allow for the explicit simulation of the electronic structure of the system but, in general, are not capable of being used in long-timescale molecular dynamics simulations and, therefore, give a more static picture of the relevant processes. Expected final online publication date for the Annual Review of Biophysics, Volume 50 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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