scholarly journals Development of a group contribution method for estimating free energy of peptides in a dodecane-water system via molecular dynamic simulations

2016 ◽  
Vol 17 (1) ◽  
Author(s):  
Camilo Andrés Mora Osorio ◽  
Andrés Fernando González Barrios
Keyword(s):  
Free Energy ◽  
Molecular Dynamic ◽  
Water System ◽  
Group Contribution ◽  
Molecular Dynamic Simulations ◽  
Group Contribution Method ◽  
Dynamic Simulations

scholarly journals Unveiling the helicity switching mechanism of a rigid two-tiered stacked architecture

RSC Advances ◽  
2019 ◽  
Vol 9 (3) ◽  
pp. 1501-1508
Author(s):  
Peng Liu ◽  
Yafei Duan ◽  
Xihui Bian ◽  
Xiaoyao Tan
Keyword(s):  
Free Energy ◽  
Molecular Dynamic ◽  
Atomic Level ◽  
Free Energy Calculations ◽  
Switching Process ◽  
Molecular Dynamic Simulations ◽  
Conformational Switching ◽  
Dynamic Simulations ◽  
Energy Calculations ◽  
Switching Mechanism

The conformational switching process of a rigid two-tiered stacked architecture has been revealed at the atomic level with the aid of molecular dynamic simulations and free-energy calculations.

scholarly journals Theoretical study of mechanisms for the hydrolytic deamination of cytosine via steered molecular dynamic simulations

RSC Advances ◽  
2018 ◽  
Vol 8 (61) ◽  
pp. 34867-34876 ◽  
Author(s):  
S. Tolosa ◽  
J. A. Sansón ◽  
A. Hidalgo
Keyword(s):  
Free Energy ◽  
Molecular Dynamic ◽  
Theoretical Study ◽  
Molecular Dynamic Simulations ◽  
Dynamic Simulations ◽  
Cytosine Deamination ◽  
Energy Profiles ◽  
Free Energy Profiles ◽  
Hydrolytic Deamination ◽  
Smd Simulations

Gibbs free energy profiles of the cytosine deamination assisted by a water molecule in a discrete aqueous medium were obtained by the application of Steered Molecular Dynamic (SMD) simulations.

scholarly journals Assignment of side-chain conformation using adiabatic energy mapping, free energy perturbation, and molecular dynamic simulations

2008 ◽  
Vol 8 (1) ◽  
pp. 25-34 ◽  
Author(s):  
Thomas M. Frimurer ◽  
Ole Hvilsted Olsen ◽  
Günther H. Peters ◽  
Morten Dahl Sørensen ◽  
Jens JØRgen Led
Keyword(s):  
Free Energy ◽  
Molecular Dynamic ◽  
Side Chain ◽  
Free Energy Perturbation ◽  
Molecular Dynamic Simulations ◽  
Dynamic Simulations ◽  
Side Chain Conformation ◽  
Energy Perturbation ◽  
Energy Mapping ◽  
Adiabatic Energy

Conformational modifications induced by internal tandem duplications on the FLT3 kinase and juxtamembrane domains

2019 ◽  
Vol 21 (34) ◽  
pp. 18467-18476 ◽  
Author(s):  
Guido Todde ◽  
Ran Friedman
Keyword(s):  
Free Energy ◽  
Protein Kinase ◽  
Molecular Dynamic ◽  
Energy Landscape ◽  
Landscape Analysis ◽  
Free Energy Landscape ◽  
Molecular Dynamic Simulations ◽  
Dynamic Simulations ◽  
Tandem Duplications

FLT3 is a protein kinase that becomes aberrantly expressed in certain leukaemias. Insertions in the form of tandem duplications activate the protein and were studied by molecular dynamic simulations and free energy landscape analysis.

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