scholarly journals Extracting Conformational Ensembles of Small Molecules from Molecular Dynamics Simulations: Ampicillin as a Test Case

Computation ◽  
2016 ◽  
Vol 4 (1) ◽  
pp. 5 ◽  
Author(s):  
Giuliano Malloci ◽  
Giovanni Serra ◽  
Andrea Bosin ◽  
Attilio Vargiu
Keyword(s):  
Molecular Dynamics ◽  
Small Molecules ◽  
Molecular Dynamics Simulations ◽  
Test Case ◽  
Conformational Ensembles ◽  
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.

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