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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 Jun 03 2019
Journal Name
Rawal Medical Journal
SUPERIOR VERSUS ANTERIOR PLATING OF MIDSHAFT CLAVICLE FRACTURE IN ADULT COMPARATIVE STUDY
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Clavicle fractures are common injuries in young, active individuals. The majority of the fractures (80% to 85%) occur in the mid-shaft of the bone and account for approximately 2.6% of all fractures. For many years the standard treatment of fracture clavicle was the "figure-of-eight" bandage but several indications for operative fixation, the position of plate fixation for clavicle fracture remains controversial. The aim of this study is to compare between anterio—inferior and anterior-superior plating of mid-shaft displaced clavicle fracture in complications, plate prominence, nonunion, malunion and range of motion. This study is a prospective study conducted in Al-Kindy teaching hospital .A total of 30 patients with fracture mid –sh

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Publication Date
Thu Dec 31 2015
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Comparative Study of New Re-Ni-Mo/Al2o3 and Conventional Hydrodesulphurization Catalyst
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New types of hydrodesulfurization (HDS) catalyst Re-Ni-Mo/ γ-Al2O3 was prepared and tested separately with two prepared conventional HDS catalysts (Ni-Mo/ γ-Al2O3 and Co-Mo//γ-Al2O3) by using a pilot plant hydrotreatment unit. Activities of three prepared hydrodesulfurization catalysts were examined in hydrodesulfurization (HDS) of atmospheric gas oil at different temperatures 275 to 350 °C and LHSV 1 to 4 h-1, the reactions conducted under constant pressure 40 bar and H2/HC ratio 500 ml/ml .Moreover, the hydrogenation of aromatic (HAD) in gas oil has been studied. HDS was much improved by adding promoter Re to the Ni-Mo/Al2O3

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Publication Date
Wed Dec 30 2015
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Comparative Study of New Re-Ni-Mo/Al2o3 and Conventional Hydrodesulphurization Catalyst
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New types of hydrodesulfurization (HDS) catalyst Re-Ni-Mo/ γ-Al2O3 was prepared and tested separately with two prepared conventional HDS catalysts (Ni-Mo/ γ-Al2O3 and Co-Mo//γ-Al2O3) by using a pilot plant hydrotreatment unit. Activities of three prepared hydrodesulfurization catalysts were examined in hydrodesulfurization (HDS) of atmospheric gas oil at different temperatures 275 to 350 °C and LHSV 1 to 4 h-1, the reactions conducted under constant pressure 40 bar and H2/HC ratio 500 ml/ml .Moreover, the hydrogenation of aromatic (HAD) in gas oil has been studied. HDS was much improved by adding promoter Re to the Ni-Mo/Al2O3 catalyst. The results showed that Re-Ni-Mo/ γ-Al2O3 have more activity in desulfurization than Ni-Mo//γ-Al2O3

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Publication Date
Thu Aug 21 2025
Journal Name
Journal Of Baghdad College Of Dentistry
An in-vitro scan electron microscope comparative study of dentine-Biodentine interface
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Background: Restoration of the gingival margin of Class II cavities with composite resin continues to be problematic, especially where no enamel exists for bonding to the gingival margin. The aim of study is to evaluate the marginal leakage at enamel and cementum margin of class II MOD cavities using amalgam restoration and modern composite restorations Filtek™ P90, Filtek™ Z250 XT (Nano Hybrid Universal Restorative) and SDR bulk fill with different restoratives techniques. Materials and method: Eighty sound maxillary first premolar teeth were collected and divided into two main groups, enamel group and cementum group (40 teeth) for each group. The enamel group was prepared with standardized Class II MOD cavity with gingival margin (1 m

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Publication Date
Tue Nov 01 2022
Journal Name
Reports Of Biochemistry And Molecular Biology
Comparative Study of New Biomarkers in Iraqi DM2 with and without Complications
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Publication Date
Sat Mar 01 2014
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Effectiveness of the organization and its role in achieving the requirements of Strategic success: A survey study of the opinions of a sample of workers at the Asia Telecom Company in Baghdad
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The research aims present to highlight the importance of creating construction Organizational appropriate to achieve strategic success and reduce many of the negative effects experienced by organizations has been developing his questionnaire especially so was distributed to a sample of workers in the Asia-cellular as sample included (60) responsive 0 and can embody intellectual dilemma following questions (What are the dimensions of the organizational infrastructure, and what are the justifications for carrying out the reform and development cleared the organizational structure to make it more flexible) to contribute to the achievement of the strategic requirements for success of the organization surveyed.
Find recommended a number o

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Publication Date
Fri Dec 31 2021
Journal Name
Political Sciences Journal
Pakistan: The most dangerous terrorist extremism hotbed (a study information, limitations, and factors)
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   Receipt date:10/27/2021    accepted date:12/15/2021     Publication date:31/12/2021

        Creative Commons License This work is licensed under a Creative Commons Attribution 4.0 International License.

The phenomenon of extremist extremism (terrorism) was one of the most prominent issues that took a large space in the twenty-first century, in which cognitive motives were mixed with strategic and ideological motives, leading to the emergence of terrorist extremi

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Publication Date
Fri Nov 01 2024
Journal Name
Egyptian Journal Of Aquatic Biology And Fisheries
Heavy Metals Levels in the Al-Shamiyah River: A Lotic Ecosystem Case Study
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Monitoring lotic ecosystems is vital for addressing sustainability issues. The Al-Shamiyah River is the primary source of water for various daily activities in the Al-Shamiyah district. This study assessed the pollution levels of the river by measuring the concentration and distribution of heavy metals—specifically chromium, cadmium, manganese, copper, zinc, and lead—in both the river's water and sediments. The concentrations of heavy metals in the water ranged from 0.05 to 1.44µg/ L for copper (Cu), 1.57 to 7.25µg/ L for manganese (Mn), 0 to 1.7µg/ L for cadmium (Cd), 0.02 to 1.33µg/ L for lead (Pb), 0.08 to 2.74µg/ L for zinc (Zn), and 0.44 to 1.84µg/ L for chromium (Cr). In the particulate phase, the concentrations ranged from

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Publication Date
Sun Dec 01 2024
Journal Name
Iraqi Journal Of Physics
Study of the Sensitivity of Carbon Quantum Dots for NO2 Gas Sensor and improve it using Graphene
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Gas sensors are essential for detecting noxious gases that have a detrimental effect on people's health and welfare. Carbon quantum dots (CQDs) are the fundamental component of gas detectors. CQDs and graphene (Gr) were prepared using the electrochemical method. The gas sensitivity of these materials was evaluated at different temperatures (150, 200, 250 °C) to assess their effectiveness. Subsequently, experiments were conducted at different temperatures to ascertain that the combination of CQDs and Gr, with various percentages of Gr and CQDs, exhibited superior gas sensitization properties compared to CQDs alone. This was evaluated based on criteria such as sensitivity, recovery time, and reaction time. Interestingly, the combination was

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Publication Date
Sun Apr 30 2017
Journal Name
Journal Of Engineering
Implementation of a Proposed Load-Shedding System Using Altera DE2 FPGA
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A load-shedding controller suitable for small to medium size loads is designed and implemented based on preprogrammed priorities and power consumption for individual loads. The main controller decides if a particular load can be switched ON or not according to the amount of available power generation, load consumption and loads priorities. When themaximum allowed power consumption is reached and the user want to deliver power to additional load, the controller will decide if this particular load should be denied receiving power if its priority is low. Otherwise, it can be granted to receive power if its priority is high and in this case lower priority loads are automatically switched OFF in order not to overload the power generation. The

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