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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
Sat Jan 21 2023
Journal Name
Indian Journal Of Health Sciences And Biomedical Research (kleu)
Vitamin D status of children at a tertiary care hospital of Agartala, North-East India: A cross-sectional study
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Publication Date
Sun Dec 15 2019
Journal Name
Al-adab Journal
La faculté articulatoire de l'apprenant irakien Dans une classe de français langue étrangère A l’université de Bagdad Etude comparative
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Publication Date
Sun Mar 28 2021
Journal Name
Journal Of The College Of Education For Women
Social Protection and its Impact on the Cohesion of Vulnerable Groups: A Field Study of a Sample Social Protection Network Beneficiaries: دينا داود محمد المولى
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Social protection meets different aspects of the needs of vulnerable groups, such as the economic, health, education, and family relations and ties in the Iraqi society. This is because vulnerable groups have suffered from social and economic influences that have negative implications on the social reality as a whole. Poverty is a case in point, which paved the way to frequent setbacks that have led to social structure instability. Accordingly, the present study aims to examine the role and effect of the Net of Social Protection Program in equally distributing social protection to curb or mitigate any negative consequnces that might happen to the poor segments and vulnerable people, who are succeptible to shocks, such as: the orphans, un

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Publication Date
Sun Mar 17 2019
Journal Name
Baghdad Science Journal
Study of Aerodynamic Surface Roughness for Baghdad City Using Signal-Level Measurements
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Roughness length is one of the key variables in micrometeorological studies and environmental studies in regards to describing development of cities and urban environments. By utilizing the three dimensions ultrasonic anemometer installed at Mustansiriyah university, we determined the rate of the height of the rough elements (trees, buildings and bridges) to the surrounding area of the university for a radius of 1 km. After this, we calculated the zero-plane displacement length of eight sections and calculated the length of surface roughness. The results proved that the ranges of the variables above are ZH (9.2-13.8) m, Zd (4.3-8.1) m and Zo (0.24-0.48) m.

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Publication Date
Sun Jan 01 2017
Journal Name
البحوث التربويةوالنفسية
Preparing a teacher’s guide for computer books for the intermediate stage according to learning styles
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Publication Date
Fri Jul 28 2023
Journal Name
Journal Of Advanced Pharmaceutical Technology & Research
Development of a spectrophotometric analytical approach for the measurement of cefdinir in various pharmaceuticals
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Publication Date
Thu Jan 06 2022
Journal Name
Chemical Papers
A solvent collection technique using dispersive liquid–liquid microextraction coupled with spectrophotometry for the trace determination of folic acid in pure, dosage forms and flaxseed
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A simple, rapid and environmentally friendly dispersive liquid–liquid microextraction method-based spectrophotometric method for the trace determination of folic acid has been developed. The proposed method is based on the formation of a deep yellow product via reaction of folic acid and 1,2-naphthoquine-4-sulfonate at pH = 9. The formed complex was extracted using a mixture of chloroform and ethanol. Then, the tiny organic droplets were measured at λ = 520 nm. At the optimum conditions, linearity was ranged from 0.05 to 1.5 μg/mL for the standard and samples, with a linear correlation coefficient of 0.9996. The detection limits were 0.02, 0.027, 0.03, 0.02 and 0.04 μg/mL for standard, tablet (5 mg), tablet (1 mg), syrup and fl

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Publication Date
Wed Oct 02 2024
Journal Name
International Development Planning Review
THE EFFECT OF EXERCISES USING A MINI SQUASH COURT ON IMPROVING SOME MOTOR ABILITIES AND LEARNING SOME BASIC SKILLS FOR PLAYERS AGED 10-12 YEARS
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Publication Date
Wed Oct 02 2024
Journal Name
International Development Planning Review
THE EFFECT OF EXERCISES USING A MINI SQUASH COURT ON IMPROVING SOME MOTOR ABILITIES AND LEARNING SOME BASIC SKILLS FOR PLAYERS AGED 10-12 YEARS
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Publication Date
Sat Feb 01 2020
Journal Name
Physics Of Fluids
Modeling the effects of slip on dipole–wall collision problems using a lattice Boltzmann equation method
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We study the physics of flow due to the interaction between a viscous dipole and boundaries that permit slip. This includes partial and free slip, and interactions near corners. The problem is investigated by using a two relaxation time lattice Boltzmann equation with moment-based boundary conditions. Navier-slip conditions, which involve gradients of the velocity, are formulated and applied locally. The implementation of free-slip conditions with the moment-based approach is discussed. Collision angles of 0°, 30°, and 45° are investigated. Stable simulations are shown for Reynolds numbers between 625 and 10 000 and various slip lengths. Vorticity generation on the wall is shown to be affected by slip length, angle of incidence,

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