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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 Jan 01 2024
Journal Name
Fifth International Conference On Applied Sciences: Icas2023
Facial deepfake performance evaluation based on three detection tools: MTCNN, Dlib, and MediaPipe
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Publication Date
Sun Jun 01 2014
Journal Name
Journal Of Economics And Administrative Sciences
Measuring and Analyzing of the Relationship between the Financial Development, Economic growth, and Poverty in Iraq with the Autoregressive Distributed lag Model framework for the period (1980-2010)
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The developed financial system is essential for increasing economic growth and poverty reduction in the world. The financial development helps in poverty reduction indirectly via intermediate channel which is the economic growth. The financial development enhancing economic development through mobilization of savings and channel them to the most efficient uses with higher economic and social returns. In addition, the economic growth reduces the poverty through two channels. The first is direct by increasing the introduction factors held by poor and improve the situations into the sectors and areas where the poor live. The second is indirect through redistribution the realized incomes from the economic growth as well as the realiz

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Publication Date
Fri Aug 24 2018
Journal Name
Indian Journal Of Physics
Study of the nuclear deformation of some even–even isotopes using Hartree–Fock–Bogoliubov method (effect of the collective motion)
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In the present research, the nuclear deformation of the Ne, Mg, Si, S, Ar, and Kr even–even isotopes has been investigated within the framework of Hartree–Fock–Bogoliubov method and SLy4 Skyrme parameterization. In particular, the deform shapes of the effect of nucleons collective motion by coupling between the single-particle motion and the potential surface have been studied. Furthermore, binding energy, the single-particle nuclear density distributions, the corresponding nuclear radii, and quadrupole deformation parameter have been also calculated and compared with the available experimental data. From the outcome of our investigation, it is possible to conclude that the deforming effects cannot be neglected in a characterization o

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Publication Date
Mon Mar 08 2021
Journal Name
Baghdad Science Journal
Theoretical study to find the thermal stress and strain generated in the Wood silica using lasers
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In this research study theory to find the stress and emotion gases in the glass as a result of exposure to pulses of the laser beam has been the study using vehicles three major on-system axes cylindrical (r, 0, z), where I took three models of glass silica glass soda glass fused and shedtwo types of lasers where the study showed that the thermal stresses and emotions ...

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Publication Date
Tue Nov 14 2017
Journal Name
Indian Journal Of Clinical Biochemistry
Visfatin, PON-1 Levels in Iraqi Hyperthyroidism Patient’s with Dyslipidemia
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Publication Date
Fri Jan 15 2010
Journal Name
Joijrnal Of College Ofeducation
Association between Insulin Resistance and Mellitus type 1 in children
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Aim of the study is to find any correlation between obesity (insulin resistance) and type I diabetes in children. Obesity and diabetes mellitus are the common health problems, and obesity is common cause of the insulin resistance. The results revealed marked increased in glucose, insulin, HbAlc and insulin resistance in obese diabetic type I patients comparing to control group they were obese and non-obese found to be within normal values for glucose, insulin, FIbAlc , and insulin resistance.

Publication Date
Thu Dec 15 2022
Journal Name
Journal Of Petroleum Research And Studies
Selection of an Optimum Drilling Fluid Model to Enhance Mud Hydraulic System Using Neural Networks in Iraqi Oil Field
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In drilling processes, the rheological properties pointed to the nature of the run-off and the composition of the drilling mud. Drilling mud performance can be assessed for solving the problems of the hole cleaning, fluid management, and hydraulics controls. The rheology factors are typically termed through the following parameters: Yield Point (Yp) and Plastic Viscosity (μp). The relation of (YP/ μp) is used for measuring of levelling for flow. High YP/ μp percentages are responsible for well cuttings transportation through laminar flow. The adequate values of (YP/ μp) are between 0 to 1 for the rheological models which used in drilling. This is what appeared in most of the models that were used in this study. The pressure loss

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Publication Date
Fri Jan 20 2023
Journal Name
Journal Of Electronic Materials
Influence of Dry and Wet Etching on AlInSb Contact Resistivity, Transfer Length, and Sheet Resistance Using Circular Transmission Model
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Publication Date
Wed Jan 01 2020
Journal Name
Proceedings Of The 2020 2nd International Conference On Sustainable Manufacturing, Materials And Technologies
The food web prey-predator model with toxin
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Publication Date
Fri Aug 30 2024
Journal Name
Iraqi Journal Of Science
The Migration Effect on an Eco-toxicant Model
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This paper proposes and studies an ecotoxicant system with Lotka-Volterra functional response for predation including prey protective region. The equilibrium points and the stability of this model have been investigated analytically both locally and globally. Finally, numerical simulations and graphical representations have been utilized to support our analytical findings

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