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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 Apr 01 2017
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Clinical Evaluation of a Formulated Econazol Nitrate as A Topical Solution
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Econazole nitrate (EN) is considered as the most effective agent for the treatment of all forms of dermatomycosis caused by dernatophytes. It was formulated as a topical solution in our laboratories. This study was designed to evaluate the effectiveness of Econazol Nitrate in the prepared formula and compared with that of commercial brand, Pevaryl®. A total of 104 patient suffering from dermatomycoses were involved in this investigation. Both formula were applied to the affected skin region in the morning and evening from week to 16 weeks with light massage until complete healing effect was achieved. The data revealed that the percentage of cured patient treated with the prepared formula and reference formula of Ecanozol Nitrate 1% so

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Publication Date
Thu Jun 15 2023
Journal Name
Journal Of Legal Sciences
Legal Protection of Computer Programs
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Computer programs are one of the most prominent features of technical progress in the field of information technology, which has raised many new issues that have not existed since the mid-twentieth century. and controls on the use of these programs by third parties, Controversy still exists about the legal nature of computer programs between those who believe that they are subject to the laws of patents and industrial property, and those who believe that they are subject to the laws of copyright protection and literary and artistic property, and the resulting difference in the scope of protection and rights established according to the legal system adopted in the application. This study comes to shed light on the legal nature of computer

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Publication Date
Wed Mar 01 2023
Journal Name
Al-khwarizmi Engineering Journal
A Methodology for Evaluating and Scheduling Preventive Maintenance for a Thermo-Electric Unit Using Artificial Intelligence
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Flow-production systems whose pieces are connected in a row may not have maintenance scheduling procedures fixed because problems occur at different times (electricity plants, cement plants, water desalination plants). Contemporary software and artificial intelligence (AI) technologies are used to fulfill the research objectives by developing a predictive maintenance program. The data of the fifth thermal unit of the power station for the electricity of Al Dora/Baghdad are used in this study. Three stages of research were conducted. First, missing data without temporal sequences were processed. The data were filled using time series hour after hour and the times were filled as system working hours, making the volume of the data relativel

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Publication Date
Thu Dec 01 2022
Journal Name
Baghdad Science Journal
A Green Synthesis of Iron/Copper Nanoparticles as a Catalytic of Fenton-like Reactions for Removal of Orange G Dye
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This research paper studies the use of an environmentally and not expensive method to degrade Orange G dye (OG) from the aqueous solution, where the extract of ficus leaves has been used to fabricate the green bimetallic iron/copper nanoparticles (G-Fe/Cu-NPs). The fabricated G‑Fe/Cu-NPs were characterized utilizing scanning electron microscopy, BET, atomic force microscopy, energy dispersive spectroscopy, Fourier-transform infrared spectroscopy and zeta potential. The rounded and shaped as like spherical nanoparticles were found for G-Fe/Cu‑NPs with the size ranged 32-59 nm and the surface area was 4.452 m2/g. Then the resultant nanoparticles were utilized as a Fenton-like oxidation catalyst. The degradation efficiency of

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Publication Date
Fri Mar 12 2021
Journal Name
Medico Legal Update
Human Cytomegalovirus Infection as a Risk Factor for Type 2 Diabetes Mellitus Development in a Sample of Iraqi Patients
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Type 2 diabetes mellitus which abbreviate as T2DM is a complex endocrine and metabolic disorder arisingfrom genetic and environmental factors interaction which in turn induce various degrees of insulin functionalalteration on peripheral tissues. Globally, T2DM has develop into a public health problem. Therefore, Thestudy included (75) patients(37 female and 38 males) suffering from T2DM who visit al-kadhimiya teachinghospital with age range 20-80 years and (70) as healthy controls with age range 20-70 years. All studiedgroups were evaluated CMV IgG by ELISA,B. urea, S. Creatinine, cholesterol and triglyceride the resultsshowed that B.urea, S.creatinine and serum cholesterol showed a non-significant differences between studiedgroup,

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Publication Date
Tue Apr 29 2025
Journal Name
Modern Sport
A Comparative Study on the Results of the Administrative Performance Skills Scale Among Heads of Sports Talent Departments in the Ministry of Youth and Sports
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Sports management is a fundamental pillar that supports sports institutions and plays a pivotal role in achieving advanced levels of success in talent development. The Talent Development Project is one of the key strategic initiatives of the Ministry of Youth and Sports. This study compares department heads with effective managerial competence to those with ineffective competence to highlight differences in performance quality. Through this comparison, the urgent need to assess the administrative performance skills of the heads of sports talent departments becomes evident, particularly their ability to lead and manage the Sports Talent Development Project. The objective is to identify strengths and weaknesses, establish a clear framework fo

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Publication Date
Thu Jun 15 2017
Journal Name
International Journal Of Computer Applications
Analytical and Numerical Study of the Temperature Distribution for a Solid Sphere subjected to a Uniform Heat Generation
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Publication Date
Wed Sep 05 2007
Journal Name
Neural Network World
A canonical generic algorithm for likelihood estimator of first order moving average model parameter
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The increasing availability of computing power in the past two decades has been use to develop new techniques for optimizing solution of estimation problem. Today's computational capacity and the widespread availability of computers have enabled development of new generation of intelligent computing techniques, such as our interest algorithm, this paper presents one of new class of stochastic search algorithm (known as Canonical Genetic' Algorithm ‘CGA’) for optimizing the maximum likelihood function strategy is composed of three main steps: recombination, mutation, and selection. The experimental design is based on simulating the CGA with different values of are compared with those of moment method. Based on MSE value obtained from bot

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Publication Date
Sun Jan 02 2011
Journal Name
Journal Of The Faculty Of Medicine Baghdad
Relation-ships of neonatal septicemia with the mean serum levels of IL-8 and IL-1 in three large hospitals in Baghdad
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Publication Date
Sun Dec 01 2019
Journal Name
2019 First International Conference Of Computer And Applied Sciences (cas)
A Comparison for Some of the estimation methods of the Parallel Stress-Strength model In the case of Inverse Rayleigh Distribution
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