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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 Aug 01 2020
Journal Name
Heat Transfer
A parametric study of a photovoltaic panel with cylindrical fins under still and moving air conditions in Iraq
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Publication Date
Wed Mar 01 2023
Journal Name
Baghdad Science Journal
Pharmacokinetic Consideration to Formulate Sustained Release Drugs: Understanding the Controlled Drug Diffusion through the Body Compartment of the Systemic Circulation and Tissue Medium-A Caputo Model
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The aim of this study is to provide an overview of various models to study drug diffusion for a sustained period into and within the human body. Emphasized the mathematical compartment models using fractional derivative (Caputo model) approach to investigate the change in sustained drug concentration in different compartments of the human body system through the oral route or the intravenous route. Law of mass action, first-order kinetics, and Fick's perfusion principle were used to develop mathematical compartment models representing sustained drug diffusion throughout the human body. To adequately predict the sustained drug diffusion into various compartments of the human body, consider fractional derivative (Caputo model) to investiga

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Publication Date
Thu Sep 01 2016
Journal Name
Journal Of Engineering
The Effect of Vehicle Body Shapes on the Near Wake Region and Drag Coefficient: A Numerical Study
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The purpose of this paper is to gain a good understanding about wake region behind the car body due to the aerodynamic effect when the air flows over the road vehicle during its movement. The main goal of this study is to discuss the effect of the geometry on the wake region and the aerodynamic drag coefficient. Results will be achieved by using two different shapes, which are the fastback and the notchback. The study will be implemented by the Computational Fluid Dynamic (CFD) by using STAR-CCM+® software for the simulation. This study investigates the steady turbulent flow using k-epsilon turbulence model. The results obtained from the simulation show that the region of the air separation behind the vehicle

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Publication Date
Tue Jan 01 2013
Journal Name
Advances In Physics Theories And Applications
Adsorption Study of Symmetrical Schiff Base Ligand 4,4’-[hydrazine-1,2-diylidenebis(methan-1-yl-1-ylidene) bis (2-methoxyphenol)] on Granulated Initiated Calcined Iraqi Montmorillonite via Columnar Method.
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The adsorption ability of Iraqi initiated calcined granulated montmorillonite to adsorb Symmetrical Schiff Base Ligand 4,4’-[hydrazine-1, 2-diylidenebis (methan-1-yl-1-ylidene)) bis (2-methoxyphenol)] derived from condensation reaction of hydrazine hydrate and 4-hydroxy-3-methoxybenzaldehyde, from aqueous solutions has been investigated through columnar method.The ligand (H2L) adsorption found to be dependent on adsorbent dosage, initial concentration and contact time.All columnar experiments were carried out at three different pH values (5.5, 7and 8) using buffer solutions at flow rate of (3 drops/ min.),at room temperature (25±2)°C. The experimental isotherm data were analyzed using Langmuir, Freundlich and Temkin equations. The monol

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Publication Date
Tue Nov 01 2016
Journal Name
Journal Of Economics And Administrative Sciences
The role of public relations in enhancing the quality of governmental service-a Field study in the Iraqi Airlines
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Abstract
        The research has discussed the public relations as dependent variable of its branch dimensions( confidence , commitment, control and satisfaction ) and the governmental service quality as independent variable of its branch dimensions (response, dependency, emphasis, tangibility and sympathy), and the research problem has represented by weakness of service quality presented to the customers dealing with company, which is observed via  field co-existence of the researcher, where he observe that the quality presented in the company services, are inappropriate with the customers expectations level, also there is weakness of attention and recognition by the

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Publication Date
Thu Feb 19 2026
Journal Name
Journal Of Economics And Administrative Sciences
The role of public relations in enhancing the quality of governmental service-a Field study in the Iraqi Airlines
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Publication Date
Thu Jan 13 2022
Journal Name
Journal Of Water And Land Development
A study of the climate and human impact on the future survival of the Al-Sannya marsh in Iraq
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Polish Academy of Sciences

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Publication Date
Fri Mar 13 2020
Journal Name
Sustainability
Consumers’ Perceptions and Attitudes toward Products Preventing Microfiber Pollution in Aquatic Environments as a Result of the Domestic Washing of Synthetic Clothes
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Microfibers released by synthetic clothes have a significant negative effect on the environment. Several solutions have been proposed and evaluated for their effectiveness, but studies have failed to address the human-centered aspects of these products. In this research, the possibilities and needs from a consumer perspective for a new filtering system for domestic washing machines were examined. First, a quantitative (questionnaire) and a qualitative (interviews and observations) exploration were done to understand the desired requirements from a user perspective. Next, the acceptance of various existing solutions for microfiber catching was investigated. To verify these requirements, a new concept was designed and evaluated with a

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Publication Date
Thu Feb 19 2026
Journal Name
Journal Of Baghdad College Of Dentistry
Evaluation of the Efficiency of Three Different Obturation Techniques to Obturate the Isthmus Area of Roots Canals Prepared by Two Different Instrumentation Techniques (An In Vitro Study)
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Background: The isthmus is a difficult area in the root canal complex to manage. The research aimed to evaluate the efficiency of three different obturation techniques (lateral condensation, EandQ (thermoplasticized gutta percha system) and Soft Core (thermoplasticized core carrier gutta percha system)) to obturate the isthmus area of roots prepared by two different instrumentation techniques (rotary ProTaper universal and ProTaper Next systems). Material and method: Sixty freshly extracted teeth were randomly divided into two main groups (A and B) of 30 teeth each. Group A was prepared by rotary ProTaper Universal whereas group B was prepared by ProTaper Next system. Each main group was then randomly subdivided into three subgroups of 10 t

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Publication Date
Sat Feb 02 2019
Journal Name
Journal Of The College Of Education For Women
The Reasons behind the decadence of the studies concerning the evening school in Salah al Deen A field study
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The Reasons behind the decadence of the studies concerning the evening school in Salah al Deen A field study

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