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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 Mar 12 2026
Journal Name
Journal Of Baghdad College Of Dentistry
Stem cells a novel approach to periodontal regeneration (A review of literature)
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In this review of literature, the light will be concentrated on the role of stem cells as an approach in periodontal regeneration.

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Publication Date
Mon Mar 08 2021
Journal Name
Surgical Neurology International
Ruptured giant aneurysm of a cortical middle cerebral artery: A case report
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Background:

Aneurysms of the cortical branches of the middle cerebral artery (MCA) are rare. They usually are secondary to traumatic or infectious etiologies and are rarely idiopathic. The specific characteristics of idiopathic aneurysms in such location are not well defined in the literature. The authors report a rare case of a ruptured giant idiopathic cortical MCA aneurysm with review of the available literature on this clinical entity.

Case Description:

A 24-year-old female presented with headache, disturbed level of consciousness, and right-sided weakness. Imaging studies showed a left frontoparietal intracer

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Publication Date
Sat Apr 01 2017
Journal Name
Journal Of Economics And Administrative Sciences
Use aggregate slide estimate additive splines estimation for the diagnosis of non-linear composite model self-regression with practical application
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Nonlinear time series analysis is one of the most complex problems ; especially the nonlinear autoregressive with exogenous variable (NARX) .Then ; the problem of model identification and the correct orders determination considered the most important problem in the analysis of time series . In this paper , we proposed splines  estimation method for model identification , then we used three criterions for the correct orders determination. Where ; proposed method used to estimate the additive splines for model identification , And the rank determination depends on the additive property  to avoid the problem of curse dimensionally . The proposed method is one of the nonparametric methods , and the simulation results give a

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Publication Date
Thu Oct 01 2020
Journal Name
Plant Archives
Taxonomical study for the species volkameria inermis l. (lamiaceae)
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Publication Date
Sun Aug 21 2022
Journal Name
International Journal Of Health Sciences
Molecular detection of fimH& mrkDgenes of strong biofilm producers & MDR Klebsiella pneumoniae
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Klebsiella pneumoniae is an adaptable pathogen that forms biofilms on a variety of surfaces. This study's objective was to identify the presence of fimbrial genes (types 1 and 3) in K. pneumoniae strains isolated from various clinical sources based on their antibiotic resistance and ability to form biofilms. According to identification utilizing the vitek 2 technology and confirmation by molecular identification targeting the 16S rRNA gene with a particular primer, forty isolates were identified from clinical specimens. The vitek 2 compact system was utilized to evaluate the antibiotic susceptibility of all the isolates. The findings revealed a range of resistance percentages, including 52.5% for Penicillin, 40.5% for Trimethoprim/S

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Publication Date
Sun Mar 04 2018
Journal Name
Baghdad Science Journal
Using Texture Analysis Image Processing Technique to Study the Effect of Microwave Plasma on the Living Tissue
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The present study is a hybrid method of studying the effect of plasma on the living tissue by using the image processing technique. This research explains the effect of microwave plasma on the DNA cell using the comet score application, texture analysis image processing and the effect of microwave plasma on the liver using texture analysis image processing. The study was applied on the mice cells. The exposure to the plasma is done by dividing the mice for four groups, each group includes four mice (control group, 20, 50, 90 second exposure to microwave plasma). The exposure to microwave plasma was done with voltage 175v and gas flow on 2 with room temperature; the statistical features are obtained from the comet score images and the textur

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Publication Date
Sun Dec 20 2020
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The use of Auditors the Islamic Financial Engineering tool for Assessing Funding Risk Management in Islamic Banks: Applied research on a sample of Islamic banks
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Experience the Islamic financial industry faces many challenges, most notably the lack of proper risk management tools that meet the requirements of legality and economic efficiency advantage from another side, so it requires the search for innovative ways to manage the risk of Islamic banking, Islamic finance industry is manufacture up-to-date, if compared with the financial industry (traditional), which increases the problematic of risk management in the Islamic financial industry nature of treatment which should be compatible with Islamic law, as well as economic efficiency, thereby Progress came the importance of research to highlight the entrance to Islamic financial engineering and the goals sought to be achieved through the use of

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Publication Date
Sat Sep 08 2018
Journal Name
International Journal Of Applied Pharmaceutics
PREPARATION AND CHARACTERIZATION OF LAFUTIDINE AS IMMEDIATE RELEASE ORAL STRIP USING DIFFERENT TYPE OF WATER-SOLUBLE POLYMER
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Objective: The objective of the present study was to design and optimize oral fast dissolving film (OFDF) of practically insoluble drug lafutidine in order to enhance bioavailability and patient compliance especially for a geriatric and unconscious patient who are suffering from difficulty in swallowing.Methods: The films were prepared by a solvent casting method using low-grade hydroxyl propyl methyl cellulose (HPMC E5), polyvinyl alcohol (PVA), and sodium carboxymethyl cellulose (SCMC) as film forming polymers. Polyethylene glycol 400 (PEG400), propylene glycol (PG) and glycerin were used as a plasticizer to enhance the film forming properties of the polymer. Tween 80 (1% solution) and poloxamer407 were used as a surfactant, citri

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Publication Date
Sun Apr 17 2016
Journal Name
جلة ابن الهيثم للعلوم الصرفةم
isolation and partial purification of cell wall lipopolysaccharides of pseduomonas areuginosa and using it as Vaccine it
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Publication Date
Mon May 01 2017
Journal Name
International Journal Of Science And Research (ijsr)
Some Properties of Mortar and Concrete Using Brick, Glass and Tile Waste as Partial Replacement of Cement
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The using of waste products as a recycled material was one of the most important studies for saving money and reduces the pollution. Mortar and concrete mixes with (10, 20 and 30)% of brick, glass and tile powder as replacement by weight of cement was investigated. The concrete mixes using brick or glass as 10%replacement of cement exhibited enhancement in compressive strength about (6, 4.7 and 2.0)% and (7.2, 5.6 and 2)% at age 7, 28 and 90 days respectively compared to reference mix. The 20% replacement of glass powder also showed an increase in the compressive strength up to (8, 6.3 and 4) %at age 7,28 and 90 days respectively compared to reference mix. Finally concrete mix using (10, 20 and 30) % tile powder as replacement of cement sho

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