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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
Wed Apr 23 2025
Journal Name
Journal Of The College Of Basic Education
A historical study of Iraqi Olympic participation for the period (1929 - 2000)
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The history of the Olympic movement in Iraq is a rich history that reflects the interest of Iraqi governments and society in sports, the social and economic conditions, and international relations, and highlights the intersection of sports and politics and the impact of global events on local sports development. Therefore, providing a valuable insight into the reality of the participation and results achieved by Iraq in the Olympic Games for the period under study helps in giving a broader understanding of Iraq’s position in the global sports community. The research aims to document the important events in the development of the Olympic movement in Iraq for the period (1929-2000) and explore the formation and development of the Iraqi Olym

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Publication Date
Thu May 25 2023
Journal Name
Results In Chemistry
Synthesis and characterization of (E)-4-(((4-(5-mercapto-1, 3, 4-oxadiazol-2-yl) phenyl) amino) methyl)-2-methoxyphenol as a novel corrosion inhibitor for mild-steel in acidic medium
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Metal corrosion is a destructive process for many industrial operations, including oil well acidizing and acid pickling. Therefore, numerous efforts made by many researchers to control the steel corrosion. In the present work, A (E)-4-(((4-(5-mercapto-1,3,4-oxadiazol-2-yl) phenyl) amino) methyl)-2-methoxyphenol (MOPM) has been synthesized and characterized as a new corrosion inhibitor for mild steel in 0.1 M hydrochloric acid. FTIR and 1 HNMR were used in the diagnosis of MOPM, while electrochemical polarization technique was employed to test the performance of inhibitor at various temperatures and inhibitor concentrations. Electrochemical studies showed that MOPM acts as a mixed-type inhibitor with a maximum inhibition efficiency of

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Publication Date
Sun Jan 01 2023
Journal Name
Results In Chemistry
Synthesis and characterization of (E)-4-(((4-(5-mercapto-1, 3, 4-oxadiazol-2-yl) phenyl) amino) methyl)-2-methoxyphenol as a novel corrosion inhibitor for mild-steel in acidic medium
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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
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
Mon Jan 01 2018
Journal Name
Journal Of The College Of Languages (jcl)
‘There is no place like home’: A Comparative Study of the Meaning of Home in The Wonderful Wizard of Oz and Peter and Wendy
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The Wonderful Wizard of Oz and Peter and Wendy present universal ideas that exist in all times, despite being written in the beginning of the 20th century. Among the most significant ones is the concept of “home”. The article discusses the essentiality of the idea of “home” where the identity of an individual shapes, and where one’s spiritual, psychological, and physical being develop. It also studies the attitudes of each protagonist towards the concept of ‘home’ based on their understanding of it and according to their gender differences. The characters in both stories tread on the path of perplexity between leaving their homes and returning to them. Peter’s world is the world of imagination while Doro

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Publication Date
Wed Dec 14 2016
Journal Name
Journal Of Baghdad College Of Dentistry
Comparative Evaluation of the Effect of Different Universal Adhesives and Bonding Techniques on the Marginal Gap of Class I Composite Restoration (A SEM Study)
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Background: With the increase in composite material use in posterior teeth, the concerns about the polymerization shrinkage has increased with the concerns about the formation of marginal gaps in the oral cavity environment. New generation of adhesives called universal adhesive have been introduced to the market in order to reduce the technique sensitive bonding procedures to give the advantage of using the bonding system in any etching protocol without compromising the bonding strength. The aim of the study was to study marginal adaptation of two universal adhesives (Single bondâ„¢ Universal and Prime and Bond elect) using 3 etching techniques under thermal cycling aging. Materials and Methods: Forty-eight sound maxillary first premola

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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
Sat Aug 01 2015
Journal Name
Journal Of Bridge Engineering
Torsional Analysis of Multicell Concrete Box Girders Strengthened with CFRP Using a Modified Softened Truss Model
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