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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 01 2023
Journal Name
Journal Of Analytical Chemistry
A Spectrophotometric Method for Tetracycline Determination in its Bulk Powder and Pharmaceutical Formulations Using Flow Injection and Batch Procedures: a Comparative Study
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A reliable and environmental analytical method was developed for the direct determination of tetracycline using flow injection analysis (FIA) and batch procedures with spectrophotometric detection. The developed method is based on the reaction between a chromogenic reagent (vanadium (III) solution) and tetracycline at room temperature and in a neutral medium, resulting in the formation of an intense brown product that shows maximum absorption at 395 nm. The analytical conditions were improved by the application of experimental design. The proposed method was successfully used to analyze samples of commercial medications and verified throughout the concentration ranges of 25–250 and 3–25 µg/mL for both FIA and batch procedures, respecti

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Publication Date
Sat Jul 01 2023
Journal Name
Heliyon
Effect of plasma surface treatment of three different CAD/CAM materials on the micro shear bond strength with resin cement (A comparative in vitro study)
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Objectives: This study aimed to evaluate and compare the effect of plasma treatment versus conventional treatment on the micro shear bond strength (μSBS), surface roughness, and wettability of three different CAD/CAM materials. Materials and methods: Sixty cylindrical specimens (5 mm diameter ×3 mm height) were prepared from three different CAD/CAM materials: Group A: Zirconia, Group B: Lithium disilicate, and Group C: Resin nano-ceramic. Each group was subdivided into two subgroups according to surface treatment used: Subgroup I: Conventional treatment, zirconia was sandblasted with Al2O3, while lithium disilicate and resin nano-ceramic were etched with hydrofluoric acid. Subgroup II: Plasma treatment, the surface of each material was tr

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Publication Date
Tue Jun 14 2016
Journal Name
Al-academy
Idealism and Realism in The Design: A Comparative Study
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At the beginning of the twentieth century distorting handling totalitarian phenomena of art, which can be called the stage of the test, transition from the theory of ideal theory and other realistic is not cushy, since it requires vision and reading and other concepts, and in light of this dialectic manifested research problem by asking the following Is affected by the design idealism and realism. Through the above mentioned questions, the researcher found rationale for addressing this problem, the study through his research, which is marked (idealism and realism in a comparative study design). And demonstrated the importance of research in the identification of the concept and the effectiveness of the two theories idealism and realism a

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Publication Date
Sun Sep 30 2012
Journal Name
Al-hiqouq
The Maintenance Contract – A Comparative Study with Islamic Jurisprudence
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Contemporary life is racing against time in its temptations and variables, and it has become shaped and changed in an amazing way in its various aspects and fields. This was facilitated by intellectual and scientific communication between civilizations, and the rapid progression in successive inventions and discoveries in the fields of science and arts of knowledge. This contributed to a great economic and commercial renaissance. Then, these economic developments entered the world into a very strong competition, which forced producers to calculate all production costs, to reach the highest profits by reducing the price of the produced commodity on the one hand, and achieving quality in appearance (especially) on the other hand. Since the ma

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Publication Date
Sun Mar 31 2024
Journal Name
Association Of Arab Universities Journal Of Engineering Sciences
Using Solid Waste as A Substitute for Raw Materials in Construction: A Review.
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The main challenge is to protect the environment from future deterioration due to pollution and the lack of natural resources. Therefore, one of the most important things to pay attention to and get rid of its negative impact is solid waste. Solid waste is a double-edged sword according to the way it is dealt with, as neglecting it causes a serious environmental risk from water, air and soil pollution, while dealing with it in the right way makes it an important resource in preserving the environment. Accordingly, the proper management of solid waste and its reuse or recycling is the most important factor. Therefore, attention has been drawn to the use of solid waste in different ways, and the most common way is to use it as an alternative

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Publication Date
Wed Sep 30 2020
Journal Name
College Of Islamic Sciences
The Breadth in the meaning of the "from Surah Maryam as a model.
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Prepositions have a key function, which is to associate parts of a sentence, called letters In addition, it adds the meanings of the verbs to the names, ie reached by them, and called by the coffin characters Qualities..

          I chose to search for the meaning of the preposition "from" in Surat Maryam to know its meanings in terms of originality and expansion, so the title of the research (the meanings of preposition "from" in terms of originality and expansion in Surat Maryam model(

 

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Publication Date
Wed Feb 18 2026
Journal Name
Journal Of Baghdad College Of Dentistry
Immunohistochemical expression of ICAM-1 and Cortactin as cell adhesive molecule and invasive markers in Hodgkin’s and non-Hodgkin’s lymphoma of the head and neck region (A comparative study)
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Background: Lymphomas are a group of diseases caused by malignant lymphocytes that accumulate in lymph nodes and cause the characteristic clinical features of lymphadenopathy. Intercellular adhesion molecule-1 (ICAM-1) (CD54) is a transmembrane glycoprotein belonging to the immunoglobulin superfamily of adhesion molecules. Cortactin was first identified as one of the major substrates for src kinase. because it localized to Cortical actin structures, The aims of this study was to evaluate and compare the immunohistochemical of ICAM-1 expression as cell adhesion molecule marker and Cortactin expression as invasive marker. Material and Methods: This study was performed on (68) formalin-fixed, paraffin-embedded blocks, histopathologically diagn

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Publication Date
Sun Mar 01 2020
Journal Name
Baghdad Science Journal
A Comparative Study on the Double Prior for Reliability Kumaraswamy Distribution with Numerical Solution
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This work, deals with Kumaraswamy distribution. Kumaraswamy (1976, 1978) showed well known probability distribution functions such as the normal, beta and log-normal but in (1980) Kumaraswamy developed a more general probability density function for double bounded random processes, which is known as Kumaraswamy’s distribution. Classical maximum likelihood and Bayes methods estimator are used to estimate the unknown shape parameter (b). Reliability function are obtained using symmetric loss functions by using three types of informative priors two single priors and one double prior. In addition, a comparison is made for the performance of these estimators with respect to the numerical solution which are found using expansion method. The

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Publication Date
Fri Jun 28 2024
Journal Name
Al-rafidain Journal Of Medical Sciences ( Issn 2789-3219 )
Synthesis, Characterization, Molecular Docking, ADMET Study, and Antimicrobial Evaluation of New Mannich Bases of Isatin–Thiazole Imine Bases
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Background: The isatin molecule is present in many natural substances, including plants and animals, and is used to prepare compounds with various biological activities. Objectives: To synthesize a new series of isatin derivatives with the expectation that they will have antimicrobial activity. Methods: Thiazole Schiff bases were synthesized from various Mannich bases of isatin to evaluate their antimicrobial properties. Initially, Mannich bases (2a–e) were synthesized by reacting isatin with formaldehyde and different secondary amines. Subsequently, they were treated with 2-aminothiazole to yield the final compounds (3a–e). Spectroscopic characterization was done via FT-IR and 1H-NMR. The antimicrobial screening was conducted o

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Publication Date
Tue Sep 30 2025
Journal Name
Iraqi Journal Of Science
A Study on Using Molasses Production Waste Powder as a Green Adsorbent for Cu (II) Ions from its Aqueous Solution
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This study utilized low-cost agricultural waste (molasses production waste powder) to extract copper ions from aqueous solutions. The present investigation explored a range of factors that influence the adsorption process, including temperature, pH, ionic strength, contact time, quantity of adsorbent, and particle size. Spectrophotometric analysis was used to determine the solution's absorbance both before and after the adsorption procedure. The Langmuir and Freundlich adsorption models were used to match the equilibrium data. The Freundlich model was determined to be the best isotherm model using the linear regression coefficient R2=0.9868. Thermodynamic parameters, including enthalpy, entropy, and Gibbs free energy, were calculate

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