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A Comparative Study for the Accuracy of Three Molecular Docking Programs Using HIV-1 Protease Inhibitors as a Model
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Flexible molecular docking is a computational method of structure-based drug design to evaluate binding interactions between receptor and ligand and identify the ligand conformation within the receptor pocket. Currently, various molecular docking programs are extensively applied; therefore, realizing accuracy and performance of the various docking programs could have a significant value. In this comparative study, the performance and accuracy of three widely used non-commercial docking software (AutoDock Vina, 1-Click Docking, and UCSF DOCK) was evaluated through investigations of the predicted binding affinity and binding conformation of the same set of small molecules (HIV-1 protease inhibitors) and a protein target HIV-1 protease enzyme. The tested sets are composed of eight receptor-ligand complexes with high resolution crystal structures downloaded from Protein Data Bank website. Molecular dockings were applied between approved HIV-1 protease inhibitors and the HIV-1 protease using AutoDock Vina, 1-Click Docking, and DOCK6. Then, docking poses of the top-ranked solution was realized using UCSF Chimera. Furthermore, Pearson correlation coefficient (r) and coefficient of determination (r2) between the experimental results and the top scored docking results of each program were calculated using Graphpad prism V9.2. After comparing saquinavir top scored binding poses of each docking program with the crystal structure, various conformational changes were observed. Moreover, according to the relative comparison between the top ranked calculated ?Gbinding values against the experimental results, r2 value of AutoDock Vina, 1-Click Docking, and DOCK6 were 0.65, 0.41, and 0.005, respectively. The outcome of this study shows that the top scored binding free energy could not produce the best pose prediction. In addition, AutoDock Vina results have the highest correlation with the experimental results.

 

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Publication Date
Mon May 11 2020
Journal Name
Journal Of Arts, Literature, Humanities And Social Sciences
The Kite Runner; A Journey of Growth
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Publication Date
Thu Dec 01 2022
Journal Name
Iraqi Journal Of Statistical Sciences
Use The Coiflets and Daubechies Wavelet Transform To Reduce Data Noise For a Simple Experiment
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In this research, a simple experiment in the field of agriculture was studied, in terms of the effect of out-of-control noise as a result of several reasons, including the effect of environmental conditions on the observations of agricultural experiments, through the use of Discrete Wavelet transformation, specifically (The Coiflets transform of wavelength 1 to 2 and the Daubechies transform of wavelength 2 To 3) based on two levels of transform (J-4) and (J-5), and applying the hard threshold rules, soft and non-negative, and comparing the wavelet transformation methods using real data for an experiment with a size of 26 observations. The application was carried out through a program in the language of MATLAB. The researcher concluded that

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Publication Date
Mon Jan 01 2018
Journal Name
Internet And Distributed Computing Systems
A Proposed Adaptive Rate Algorithm to Administrate the Video Buffer Occupancy for Smooth Video Streaming
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Publication Date
Tue Jan 01 2019
Journal Name
Technologies And Materials For Renewable Energy, Environment And Sustainability: Tmrees19gr
Theoretical calculations involving a standard neutron yield distribution for the T-T nuclear fusion reaction
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A standard theoretical neutron energy flux distribution is achieved for the triton-triton nuclear fusion reaction in the range of triton energy about ≤10 MeV. This distribution give raises an evidence to provide the global calculations including the characteristics fusion parameters governing the T-T fusion reaction.

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Publication Date
Mon Dec 03 2018
Journal Name
The Iraqi Postgraduate Medical Journal
Operative Treatment by Plate and Screws Versus Conservative Treatment of Closed Displaced Fracture of the Mid Third of Clavicle in Adults: Comparative Study
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BACKGROUND: Clavicle fractures are common injuries in young active individuals, the mid third of the clavicle is most commonly fractured part(80% of clavicle fracture) OBJECTIVE: To compare the outcomes of operative and non operative management of displaced and or comminuted closed fracture of the mid third of clavicle in young adults PATIENTS AND METHODS: This prospective observational study of 24 patients of fracture of the mid third of the clavicle was conducted in Alkindy teaching hospital from July 2015 to January 2017 and divided into two groups; one managed by operative treatment with plate and screws and the other by non operative sling immobilization after taking the consent and the patients were seen at 2, 4, 6 weeks,3, 6, and 9 m

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Publication Date
Thu Nov 18 2021
Journal Name
Iraqi Journal Of Physics
The study of nuclear structure for some nuclei
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An analytical form of the ground state charge density distributions
for the low mass fp shell nuclei ( 40  A  56 ) is derived from a
simple method based on the use of the single particle wave functions
of the harmonic oscillator potential and the occupation numbers of
the states, which are determined from the comparison between theory
and experiment.
For investigating the inelastic longitudinal electron scattering form
factors, an expression for the transition charge density is studied
where the deformation in nuclear collective modes is taken into
consideration besides the shell model space transition density. The
core polarization transition density is evaluated by adopting the
shape of Tassie mod

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Publication Date
Mon Oct 01 2018
Journal Name
Iraqi Journal Of Physics
The study of nuclear structure for some nuclei
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 An analytical form of the ground state charge density distributions
for the low mass fp shell nuclei ( 40  A  56 ) is derived from a
simple method based on the use of the single particle wave functions
of the harmonic oscillator potential and the occupation numbers of
the states, which are determined from the comparison between theory
and experiment.
For investigating the inelastic longitudinal electron scattering form
factors, an expression for the transition charge density is studied
where the deformation in nuclear collective modes is taken into
consideration besides the shell model space transition density. The
core polarization transition density is evaluated by adopting the
shape of Tass

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Publication Date
Tue Dec 27 2022
Journal Name
Chemical Papers
Synthesis, characterization, and application of external gelation of sodium alginate nanoparticles in molecular imprinting for separation and drug delivery of tenoxicam
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Publication Date
Sat Jun 01 2024
Journal Name
Results In Engineering
Stability analysis for the phytoplankton-zooplankton model with depletion of dissolved oxygen and strong Allee effects
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Publication Date
Tue Apr 16 2024
Journal Name
Ecancermedicalscience
Prostate cancer across four countries in the Middle East: a multi-centre, observational, retrospective and prognostic study
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