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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
Thu Dec 28 2023
Journal Name
Journal Européen Des Systèmes Automatisés
Design of a Hybrid Adaptive Controller for Series Elastic Actuators of Robots
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Publication Date
Mon Sep 09 2024
Journal Name
مداد الاداب
Lexical Stylistic Analysis of Two ‎Extracts from Tale of Two Cities: ‎A Contrastive Study
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Since the time it emerged, stylistics, as a field of knowledge which ‎combines both linguistics and literature, acquired a special status in the ‎linguistic arena. Its significance in complementing the meaning ‎delivered by linguistic means has been proven and acknowledged ‎through numerous stylistic analytic attempts of different literary works ‎and in different languages. The question put forward in this paper is ‎whether or not the stylistic analysis can work as effectively on translated ‎texts as it does on the original ones without having the results reached ‎by the analysis distorting the meaning of the original text. An attempt to ‎investigate this question is made herein by conducting a lexical stylistic ‎analysi

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Publication Date
Tue Sep 15 2020
Journal Name
Arab World English Journal
A Cognitive-Semantic Analysis of Preposition on: An Experimental Study at University of Baghdad
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Publication Date
Mon Jan 01 2018
Journal Name
International Journal Of Surgery Open
Effectiveness of conservative management of uncomplicated acute appendicitis: A single hospital based prospective study
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<bold>ABSTRACT</bold> <sec> <title>Background:

Acute appendicitis is one of the commonest causes of acute abdomen. There is a wide discussion and controversy on the surgical and nonsurgical treatment of acute uncomplicated appendicitis. The aim of this study was to evaluate the efficacy and outcomes of the conservative management of selected cases of acute appendicitis with an antibiotic first plan.

Patients and methods:

This was a single hospital-based prospective study with a durat

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Publication Date
Fri Feb 27 2026
Journal Name
Journal Of Baghdad College Of Dentistry
Effect of systemic administration of Simvastatin on dental implant stability: A random clinical study
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Background: the primary objective for many researches carried out in dental implantology was to reduce the period needed for functional implant loading, simvastatin (cholesterol lowering medication) had many pleiotropic effects, one of which was increasing bone density around titanium implants (1) and subsequently establishing faster osseointegrated dental implants (2,3). This study aims to reduce the period of time needed to establish secondary stability of dental implant measured in ISQ (Implant Stability Quotient) by investigating the effect of orally administered simvastatin on bone. Materials and methods: simvastatin tablets (40mg/day for three months) were administered orally for 11 healthy women aged (40-51) years old who received 1

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Publication Date
Thu Dec 30 2021
Journal Name
Al-kindy College Medical Journal
Impact of different sources of noise exposure on hearing impairment: A cross- sectional study
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Background: Mental health is integrated into PHC as a strategy of WHO to fill the gap in mental health treatment. Part of this strategy needs a level of task shifting so that mental health care is provided by different level of PHC workers and not only specialists such as psychiatrists and psychologists.

Objectives: To assess the knowledge and attitudes of family doctors regarding the provision of psychological health in PHCC and if there is an association between the certificates of these family doctors and their Knowledge and attitudes to psychological health.

Subjects and Methods:  A cross-sectional descriptive study with analytic elements was conducted in 8 famil

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Publication Date
Mon Dec 30 2024
Journal Name
Gsc Biological And Pharmaceutical Sciences
Taxonomic study of a cultivated plant of genus Zanthoxylum l. 1753 (Rutaceae) in Iraq
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Zanthoxylum L. 1753 belongs to the family Rutaceae. The plant, with its forest green color and with its distinctive fragrance attracted the attention of the study, specially it was an exotic to the environment of Iraq. Zanthoxylum is an exotic plant produced to Iraq and planted in gardens as an ever-green aromatic plant named (BUKHUR HINDI), as it is known among sellers and farmers in Iraq, because of the aromatic smell that emanated from the leaves and resembles Indian incense. The plant adapted to environmental conditions and succeeded in growing and blooming. It was examined and diagnosed for the first time in Iraq as Zanthoxylum beechyanum K. Koch. (Chinese pepper tree). Morphological characteristics and anatomical characteristi

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Publication Date
Wed Jun 01 2022
Journal Name
Canadian Journal Of Chemistry
Hydrogenation of pyridine and hydrogenolysis of piperidine over $γ$-Mo2N catalyst: a DFT study
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Increasing demands on producing environmentally friendly products are becoming a driving force for designing highly active catalysts. Thus, surfaces that efficiently catalyse the nitrogen reduction reactions are greatly sought in moderating air-pollutant emissions. This contribution aims to computationally investigate the hydrodenitrogenation (HDN) networks of pyridine over the γ-Mo2N(111) surface using a density functional theory (DFT) approach. Various adsorption configurations have been considered for the molecularly adsorbed pyridine. Findings indicate that pyridine can be adsorbed via side-on and end-on modes in six geometries in which one adsorption site is revealed to have the lowest adsorption energy (–45.3 kcal/mol). Over a nitr

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Publication Date
Wed Oct 03 2012
Journal Name
Journal Of Kufa For Chemical Science
A study of Adsorption of Acetone and 2- Butanone on Iraqi Siliceouns Rocks Powder
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Adsorption of Acetone and 2-Butanone on Iraqi siliceouns rocks powder have been investigated. UV technique has been used to determine the adsorption isotherms. The results showed that the adsorption isotherms obeyed Freundlich adsorption equation. The results showed that the adsorption increases with increasing acidity of solutions. The adsorption was exothermic process, increasing temperature leads to decreasing adsorption. H,  S, G were calculated

Publication Date
Wed Dec 15 2021
Journal Name
Journal Of Physics: Conference Series
Pretreated Fishbone as Low Cost-Adsorbent for Cationic Dye Adsorption from Aqueous Solutions: Equilibrium, Optimization, Kinetic and Thermodynamic Study
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The present study investigated the use of pretreated fish bone (PTFB) as a new surface, natural waste and low-cost adsorbent for the adsorption of Methyl green (MG, as model toxic basic dye) from aqueous solutions. The functional groups and surface morphology of the untreated fish bone (FB) and pretreated fish bone were characterized using Fourier transform infrared (FTIR), scanning electron microscopy (SEM) and Energy dispersive X-ray spectroscopy (EDS),respectively. The effect of operating parameters including contact time, pH, adsorbent dose, temperature, and inorganic salt was evaluated. Langmuir, Freundlich and Temkin adsorption isotherm models were studied and the results showed that the adsorption of basic dye followed Freundlich iso

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