Molecular Modeling Study of Dihydrofolate Reductase Inhibitors. Molecular Dynamics Simulations, Quantum Mechanical Calculations, and Experimental Corroboration

2013 ◽  
Vol 53 (8) ◽  
pp. 2018-2032 ◽  
Author(s):  
Rodrigo D. Tosso ◽  
Sebastian A. Andujar ◽  
Lucas Gutierrez ◽  
Emilio Angelina ◽  
Ricaurte Rodríguez ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Modeling ◽  
Molecular Dynamics Simulations ◽  
Dihydrofolate Reductase ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
Reductase Inhibitors ◽  
Dynamics Simulations ◽  
Dihydrofolate Reductase Inhibitors ◽  
Experimental Corroboration

scholarly journals A molecular dynamics simulation study on the propensity of Asn-Gly-containing heptapeptides towards β-turn structures: Comparison with ab initio quantum mechanical calculations

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0243429
Author(s):  
Dimitrios A. Mitsikas ◽  
Nicholas M. Glykos
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulation ◽  
Quantum Mechanical ◽  
Type I ◽  
Quantum Mechanical Calculations ◽  
Water Solvent ◽  
Simulation Protocol ◽  
Dynamics Simulations

Both molecular mechanical and quantum mechanical calculations play an important role in describing the behavior and structure of molecules. In this work, we compare for the same peptide systems the results obtained from folding molecular dynamics simulations with previously reported results from quantum mechanical calculations. More specifically, three molecular dynamics simulations of 5 μs each in explicit water solvent were carried out for three Asn-Gly-containing heptapeptides, in order to study their folding and dynamics. Previous data, based on quantum mechanical calculations within the DFT framework have shown that these peptides adopt β-turn structures in aqueous solution, with type I’ β-turn being the most preferred motif. The results from our analyses indicate that at least for the given systems, force field and simulation protocol, the two methods diverge in their predictions. The possibility of a force field-dependent deficiency is examined as a possible source of the observed discrepancy.

Gauging van der Waals interactions in aqueous solutions of 2D MOFs: when water likes organic linkers more than open-metal sites

2021 ◽  
Vol 23 (4) ◽  
pp. 3135-3143
Author(s):  
Mohammad R. Momeni ◽  
Zeyu Zhang ◽  
David Dell'Angelo ◽  
Farnaz A. Shakib
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solutions ◽  
Molecular Dynamics Simulations ◽  
Van Der Waals ◽  
Van Der Waals Interactions ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
Layered Architecture ◽  
Open Metal Sites ◽  
Dynamics Simulations

Periodic quantum mechanical calculations combined with classical molecular dynamics simulations are employed to probe stability of layered architecture of 2D MOFs and show how stability and conductivity are affected by the nature of organic linkers.

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