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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 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 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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Publication Date
Tue Jan 01 2019
Journal Name
Indian Journal Of Public Health Research & Development
Loss of the Epigenetically Inactivated-X-Chromosome (Barr Body) a Potential Biomarker for Breast Cancer Development
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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 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
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
Tue Feb 17 2026
Journal Name
Al–bahith Al–a'alami
HUMAN MODELING IN THE IRAQI PRESS: (A Survey of Human Modeling for March And April 2011)
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This research deals with what so called concept of The Human Model and how Iraqi Media concerns of this concept practically as it plays a key role in attracting readers, on the first hand. On the second, it is important to shed light on the scientific desire of the Iraqi Media and how it deals with this contemporary trend especially in editorial media.

The importance of the research stems from the fact that it alerts to a new stream of modern trends in journalistic writing, according to many modern Arab and foreign media studies; and to the importance of employing human modeling in dealing with facts, events, issues and problems in various editorial arts within their effective influence in concilia

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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
Thu Oct 01 2020
Journal Name
Journal Of Engineering Science And Technology
Gamipog: A deterministic genetic multi-parameter-order strategy for the generation of variabLE STRENGTH COVERING ARRAYS
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Publication Date
Mon Jan 01 2024
Journal Name
Malaysian Journal Of Nursing
Experiences of Nurses in Providing Care for Patients on the Cancer Journey: A Cross-Sectional Survey
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