scholarly journals Free Energy Profiles of Binding Processes of HIV-1 Protease- 2AH/4AH by Potential of Mean Force Simulations

2017 ◽  
Vol 5 (1) ◽  
pp. 19-26
Author(s):  
Yuxin Zhang
Keyword(s):  
Free Energy ◽  
Potential Of Mean Force ◽  
Energy Profiles ◽  
Hiv 1 ◽  
Free Energy Profiles

scholarly journals Free Energy Profiles along Consensus Normal Modes Provide Insight into HIV-1 Protease Flap Opening

2011 ◽  
Vol 7 (8) ◽  
pp. 2348-2352 ◽  
Author(s):  
Paulo R. Batista ◽  
Gaurav Pandey ◽  
Pedro G. Pascutti ◽  
Paulo M. Bisch ◽  
David Perahia ◽  
...  
Keyword(s):  
Free Energy ◽  
Normal Modes ◽  
Energy Profiles ◽  
Insight Into ◽  
Hiv 1 ◽  
Free Energy Profiles

MOLECULAR SIMULATION OF α-TOCOPHEROL PASSING ACROSS DPPC LIPID USING POTENTIAL OF MEAN FORCE AND ACCELERATED MOLECULAR DYNAMICS METHOD

2013 ◽  
Vol 12 (08) ◽  
pp. 1341011 ◽  
Author(s):  
FANCUI MENG
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Binding Free Energy ◽  
Computation Time ◽  
Potential Of Mean Force ◽  
Accelerated Molecular Dynamics ◽  
Energy Profiles ◽  
Lipid System ◽  
Dynamics Method ◽  
Free Energy Profiles

In this paper the process of α-tocopherol (TCP) passing across DPPC membrane was simulated using both the potential of mean force (PMF) and the accelerated molecular dynamics (aMD) methods, respectively. Energy properties, hydrogen bonds and orientation have been compared between these two methods and several conclusions have been obtained. The results indicate that TCP tends to stay at z = 1.2 nm of lipid bilayer. The binding free energy profiles of these two methods are alike. All these show that aMD could obtain comparable results as PMF method, while needs less computation time and resources. Therefore, aMD method could be used as an alternative method for prediction of transport properties of drug-lipid system.

scholarly journals Particle Diffusivity and Free-Energy Profiles in Hydrogels from Time-Resolved Penetration Data

2021 ◽  
Author(s):  
Amanuel Wolde-Kidan ◽  
Anna Herrmann ◽  
Albert Prause ◽  
Michael Gradzielski ◽  
Rainer Haag ◽  
...  
Keyword(s):  
Free Energy ◽  
Time Resolved ◽  
Energy Profiles ◽  
Penetration Data ◽  
Free Energy Profiles

Free energy profile analysis to identify factors activating the aggregation-induced emission of a cyanostilbene derivative

2021 ◽  
Author(s):  
Norifumi Yamamoto
Keyword(s):  
Free Energy ◽  
Profile Analysis ◽  
Energy Profile ◽  
Contributing Factors ◽  
Free Energy Profile ◽  
Aggregation Induced Emission ◽  
Energy Profiles ◽  
Free Energy Profiles

The contributing factors that cause the aggregation-induced emission (AIE) are determined by identifying characteristic differences in the free energy profiles of the AIE processes of the AIE-active E-form of CN-MBE and the inactive Z-form.

scholarly journals Reconstructing the Free Energy Profiles Describing the Switching Mechanism of a pH-Dependent DNA Nanodevice from ABMD Simulations

2021 ◽  
Vol 11 (9) ◽  
pp. 4052
Author(s):  
Alice Romeo ◽  
Mattia Falconi ◽  
Alessandro Desideri ◽  
Federico Iacovelli
Keyword(s):  
Free Energy ◽  
Double Helix ◽  
Minimum Energy ◽  
Switching Mechanism ◽  
Linker Length ◽  
Energy Profiles ◽  
Functional Dna ◽  
Triplex Forming Oligonucleotide ◽  
Dynamics Simulations ◽  
Free Energy Profiles

The pH-responsive behavior of six triple-helix DNA nanoswitches, differing in the number of protonation centers (two or four) and in the length of the linker (5, 15 or 25 bases), connecting the double-helical region to the single-strand triplex-forming region, was characterized at the atomistic level through Adaptively Biased Molecular Dynamics simulations. The reconstruction of the free energy profiles of triplex-forming oligonucleotide unbinding from the double helix identified a different minimum energy path for the three diprotic nanoswitches, depending on the length of the connecting linker and leading to a different per-base unbinding profile. The same analyses carried out on the tetraprotic switches indicated that, in the presence of four protonation centers, the unbinding process occurs independently of the linker length. The simulation data provide an atomistic explanation for previously published experimental results showing, only in the diprotic switch, a two unit increase in the pKa switching mechanism decreasing the linker length from 25 to 5 bases, endorsing the validity of computational methods for the design and refinement of functional DNA nanodevices.

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