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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 16 2025
Journal Name
مجلة كلية التربية الاساسية
A MINI-REVIEW ON THE FABRICATION OF EXPANDED GRAPHITE AND ITS METAL OXIDE COMPOSITES FOR THE PHOTODEGRADATION OF DYES
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This mini review provides an overview of methods for manufacturing expanded graphite (EGT) and the use of its composites with metal oxides in the field of photodegradation of dyes. Dyes from textile manufacturing represent a significant environmental pollution problem in waterways worldwide, highlighting the need for environmentally friendly and efficient technologies to remove dyes from industrial and local wastewater. Photodegradation technologies offer a low-cost, sustainable solution with minimal secondary pollution. Carbon-based materials, such as expanded graphite, are advantageous in enhancing catalytic activity. Accordingly, this review will explore the different fabrication techniques of expanded graphite and summarize the recent d

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Publication Date
Sun Jun 05 2016
Journal Name
Baghdad Science Journal
A novel online coupling of ion selective electrode with the flow injection system for the determination of vitamin B1
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A simple, fast, selective of a new flow injection analysis method coupled with potentiometric detection was used to determine vitamin B1 in pharmaceutical formulations via the prepared new selective membranes. Two electrodes were constructed for the determination of vitamin B1 based on the ion-pair vitamin B1-phosphotungestic acid (B1-PTA) in a poly (vinyl chloride) supported with a plasticized di-butyl phthalate (DBPH) and di-butyl phosphate (DBP). Applications of these ion selective electrodes for the determination of vitamin B1 in the pharmaceutical preparations for batch and flow injection systems were described. The ion selective membrane exhibited a near-Nernstian slope values 56.88 and 58.53 mV / decade, with the linear dy

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Publication Date
Sun Sep 03 2017
Journal Name
Baghdad Science Journal
A study of histological changes in the Diaphragm of male albino mice administered with aqueous extract of chamomileflowers Chamomillarecutita
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The chamomile is one of the most important medicinal plants recommended for treatment of asthma and some respiratory system diseases. This research was designed to research the effects of aqueous extract of chamomillarecutita on histological structure of Diaphragm of albino mice. The study included 40 male albino mice Musmusculus, their age ranged from (5-7) weeks.The mices were divided randomly to 5 groups and oral administered with 1 ml every day for 10 days:- First Group G1: consider as control group and treated with normal saline,Second Group G2: was treated with aqueous extract of chamomile with concentration of 3 gm /100 ml D.W, Third Group G3: was treated with aqueous extract of chamomile with concentration of 5 gm /100 ml D.W.Fourth

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Publication Date
Fri Jun 24 2022
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The role of incentive legislation in job creativity: An applied study of a sample of Babylon Technical Institute employees
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The Incentives legislation aims to raise the efficiency of job performance of all kinds through optimal investment of human resources and their capabilities to raise or increase and production influence and provide distinguished and creative services such as The Incentives Law of Productive Ministries Employees No. 20 of 1993 and instructions issued by ministries and relevant Facilities regarding incentives for their affiliates based on provisions Public Companies Law and the instructions of the Higher Education Fund issued by the Ministry of Higher Education and Scientific Research. The human element is the most unstable and complex element of production as it is characterized by a set of feelings and emotions that is expresses

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Publication Date
Tue Jun 01 2021
Journal Name
Arab Researcher
The Civil Liability of Hotels toward Victims of Sex Trafficking – A Study in Light of Iraqi and U.S. Law
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In view of the large profits made by the sex trade on the one hand, and the minor penalties imposed on the traffickers (brokers) compared with the severe penalties imposed on the drug trade and illegal weapons, on the other hand, this trade has become popular and spread in most countries of the world, and the cornerstones of this trade and A safe haven for them is hotels, especially luxury ones with international brands where their guests are rich and some may look for sex for money. Given the great physical and psychological damage to the victims, this research highlights the civil liability of hotels towards these victims in US and Iraqi law.In order not to limit the

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Publication Date
Wed Mar 10 2021
Journal Name
Baghdad Science Journal
A new approach for the topical treatment of acne vulgaris by clindamycin HCL supported on kalion
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Has been studied both processes Almetzaz and extortion of a substance Alklanda Maysan different amounts of Alcaúlan Guy 70% alcohol solution using the method when the wavelength

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Publication Date
Wed Sep 01 2010
Journal Name
The International Journal Of Biochemistry & Cell Biology
A plate-based assay system for analyses and screening of the Leishmania major inositol phosphorylceramide synthase
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Sphingolipids are key components of eukaryotic membranes, particularly the plasma membrane. The biosynthetic pathway for the formation of these lipid species is largely conserved. However, in contrast to mammals, which produce sphingomyelin, organisms such as the pathogenic fungi and protozoa synthesize inositol phosphorylceramide (IPC) as the primary phosphosphingolipid. The key step involves the reaction of ceramide and phosphatidylinositol catalysed by IPC synthase, an essential enzyme with no mammalian equivalent encoded by the AUR1 gene in yeast and recently identified functional orthologues in the pathogenic kinetoplastid protozoa. As such this enzyme represents a promising target for novel anti-fungal and anti-protozoal drugs. Given

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Publication Date
Sat Jul 08 2017
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
A Highly Sensitive Kinetic-Spectrophotometric Method for the Assay of Carbamazepine in Pure and Commercial Tablet
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The study aimed to recommend a new spectrophotometric-kinetic method for determination of carbamazepine (CABZ) in its pure form and pharmaceutical forms. The proposed procedure based on the coupling of CABZ with diazotized sulfanilic acid in basic medium to yield a colored azo dye. Factors affecting the reaction yield were studied and the conditions were optimized. The colored product was followed spectrophotometrically via monitoring its absorbance at 396 nm. Under the optimized conditions, two method (the initial rate and fixed time (10 minute)) were applied for constructing the calibration graphs. The graphs were linear in concentration ranges 2.0 to 18.0 µg.mL-1 for both methods. The proposed was applied successfully in

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Publication Date
Wed Aug 18 2021
Journal Name
Chemical Papers
Analytical methods for the identification of micro/nano metals in e-cigarette emission samples: a review
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Publication Date
Wed Jun 01 2022
Journal Name
Baghdad Science Journal
A Fuzzy Dynamic Programming for the Optimal Allocation of Health Centers in some Villages around Baghdad
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The Planning and Resource Development Department of the Iraqi Ministry of Health is very interested in improving medical care, health education, and village training programs. Accordingly, and through the available capabilities of the ministry, itdesires to allocate seven health centers to four villages in Baghdad, Iraq therefore the ministry needs to determine the number of health centers allocated to each of these villages which achieves the greatest degree of the overall effectiveness of the seven health centers in a fuzzy environment. The objective of this study is to use a fuzzy dynamic programming(DP) method to determine the optimal allocation of these centers, which allows the greatest overall effectiveness of these health centers

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