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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 May 01 2019
Journal Name
Heliyon
Toward liveable commercial streets: A case study of Al-Karada inner street in Baghdad
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Publication Date
Sun Dec 01 2019
Journal Name
Baghdad Science Journal
Adsorption of Some Alephatic Dicarboxylic Acids on Zinc Oxide: A kinetic and Thermodynamic Study
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The adsorption of Malonic acid, Succinic acid, Adipic acid, and Azelaic acid from their aqueous solutions on zinc oxide surface were investigated. The adsorption efficiency was investigated using various factors such as adsorbent amount, contact time, initial concentration, and temperature. Optimum conditions for acids removal from its aqueous solutions were found to be adsorbent dose (0.2 g), equilibrium contact time (40 minutes), initial acids concentration (0.005 M). Variation of temperature as a function of adsorption efficiency showed that increasing the temperature would result in decreasing the adsorption ability. Kinetic modeling by applying the pseudo-second order model can provide a better fit of the data with a greater correla

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Publication Date
Sun Jul 01 2018
Journal Name
Vacuum
Stability, electronic and vibrational properties of GaAlN wurtzoid molecules and nanocrystals: A DFT study
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Publication Date
Mon Nov 24 2025
Journal Name
Journal Of Baghdad College Of Dentistry
Interleukine-6 Level in Saliva of Patients with Chronic Periodontitis: A Case-Control Study
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Background:Periodontal diseases are infectious diseases in which periodontalpathogens trigger chronic inflammatory and immune responses. Interleukine-6 is a multifunctional cytokine playing a central role in inflammation and tissue injury.The aim of the study IS to determine the level of Interleukin-6(IL-6) in saliva of patients with chronic periodontitis compared to healthy subjects. Materials and Methods:The total subjects of the present study is 60, divided into 3 groups; 20 patients with chronic periodontitis with pocket depth(PD ≥4 mm)(group I), 20 patients with pocket depth(PD <4 mm) with clinical attachment loss (group II), and 20 healthy controls with pocket probing depth (PPD ≤ 3 mm) without clinical attachment loss (g

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Publication Date
Sun Jun 05 2016
Journal Name
Baghdad Science Journal
Synthesis and Characterization of Cu(I)-Folic Acid Complex A Theoretical and Experimental Study
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Copper (I) complex containing folic acid ligand was prepared and characterized on the basis of metal analyses, UV-VIS, FTIR spectroscopies and magnetic susceptibility. The density functional theory (DFT) as molecular modeling calculations was used to determine the donor atoms of folic acid ligand which appear clearly at oxygen atoms binding to hydrogen. Detection of donation sights is supported by theoretical parameters such as geometry, mulliken population, mulliken charge and HOMO-LUMO gap obtained by DFT calculations.

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Publication Date
Wed Dec 11 2024
Journal Name
Journal Of Emergency Medicine, Trauma And Acute Care
Mobile application to develop nurses’ knowledge of pediatric cardiopulmonary resuscitation: A quasi-experimental study
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Background: Traditional teaching methods of cardiopulmonary resuscitation (CPR) are not effective for most learners today. They may lead to lack of retention of survival skills and poor outcomes. Various methods are adopted to provide optimal, effective, and attractive teaching methods. Application (app)-based teaching can be used as an alternative way for learners to develop their knowledge and skills. Despite the large number of professional and nonprofessional trainee members, the high quality of CPR is still not fulfilled. Technology-based learning can prove to be an effective way to teach medical subjects such as pediatric cardiac resuscitation, which require an optimal teaching environ

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Publication Date
Mon Nov 24 2025
Journal Name
Al–bahith Al–a'alami
DICTION (IN ARAB SATELLITE CHANNELS) A SIGNAL SYSTEM : (study of written And oral patterns)
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Communication has seen a big advancement through ages; concepts, procedures and technologies, it has also seen a similar advancement of language. What unites language and media is the fact that each one of them guides and contributes to the other; media exists and results from language and from the other sign systems, and what strengthens this connection is the symbolic language system, as media helps it by providing knowledge and information. The change that occurred through time must leave a significant trace in the media, for example Diction, which has changed concerning development and growth, also the ways and mediums of media have become manifold and widespread. This change affected the recipient whether it was a reader, listener o

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Publication Date
Thu Feb 01 2024
Journal Name
Baghdad Science Journal
A Kinetic Study on Microwave- assisted Extraction of Bioactive Compounds from Rosmarinus Officinalis L
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Due to the importance of the extraction process in many engineering and medical industries, in addition to great interest in medicinal plants, in this research, microwave-assisted extraction has been applied to extract some active compounds from Rosmarinus officinalis leaves.  The optimal extraction conditions were then determined by calculating the ratio and extraction efficiency. The process has also been described through kinetic study by applying five  kinetic models, the Hyperbolic diffusion model,  Power low model, the First order reaction  model, Elovich's model, and Fick's second law diffusion model and determining their compatibility with the studies operation, and determining the kinetic constants for each model. The result

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Publication Date
Wed Feb 20 2019
Journal Name
Political Sciences Journal
Article Structural violence: A study In Johann Galtung's theory of explanation he violence t
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This study deals with the subject of violence, but from another perspective, it has not been emphasized in contemporary studies of violence in Arabic and raqi universities, which is the structural or institutional aspect of violence. Traditional studies have focused their analysis of violence on the direct side the violence, The other side of the violence is the hidden violence, which is characterized by a lack of clarity of the underlying factors and its effects are not arises, which makes it the most serious violence, which requires a deep research into the social, political, economic, cultural and psychological structure of society (individuals and institutions). This study was based on the theory of the Norwegian scientist (J

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Publication Date
Tue Oct 01 2019
Journal Name
Safety Science
Perceived management commitment and psychological empowerment: A study of intensive care unit nurses’ safety
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