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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
Tue Sep 01 2020
Journal Name
Baghdad Science Journal
A Comparative Study on the Active Constituents, Antioxidant Capacity and Anti-Cancer Activity of Cruciferous Vegetable Residues
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This study is pointed out to estimate the effectiveness of two solvents in the extraction and evaluating the active ingredients and their antioxidant activity as well as anti-cancer efficiency. Therefore, residues from four different Brassica vegetables viz. broccoli, Brussels sprout, cauliflower, and red cherry radish were extracted using two procedures methods: methanolic and water crude extracts. Methanol extracts showed the highest content of total phenolic (TP), total flavonoids (TF), and total tannins (TT) for broccoli and Brussels sprouts residues. Methanolic extract of broccoli and Brussels sprouts residues showed the highest DPPH· scavenging activity (IC50 = 15.39 and 18.64 µg/ml). The methanol and water ex

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Publication Date
Sat Dec 01 2018
Journal Name
Al-khwarizmi Engineering Journal
Production of Protease Enzyme from Wheat Straw
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      Protease enzyme production was studied and optimized as  a first step to collect information about solid state fermenter) to produce protease enzyme. A local isolated Aspergillus niger was used for this study with constant spores feeding in every experiment at (105/g). Experiments carried out in conical flasks with (250 ml) containing (10 g) of wheat straw as a substrate with different conditions included temperature, pH, hydration ratio, and fermentation time, the results comprised by measuring protease activity (u). The results showed that the best activity can be obtained at (T = 32°C, t= 100 hrs, pH= 2.5 and hydration ratio is 1:3). On the other hand the results is courage to p

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Publication Date
Sat Jun 06 2020
Journal Name
International Journal Of Psychosocial Rehabilitation
A comparative study of the mechanical and electrical activities of the heart according to the energy systems of advanced players
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The study aims to identify the mechanical and electrical activities of the heart according to the energy systems of advanced players and to detect the differences between the energy systems in terms of the mechanical and electrical activities of the heart for advanced players. It was clear from the results of the significance of the differences between the three groups according to the energy systems of the advanced players in all research variables that (the non-oxygenic system "Lactic"), which represents the advanced players in the arches (800 m, 1500 m) was the first in most tests of mechanical and electrical activities of the heart, which is (Margaria-Kalamen, Wingate, systolic muscle strength of the heart FC, Stroke Volume SV

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Publication Date
Tue Dec 22 2020
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Accounting Disclosure for non-current intangible assets according to international accounting standard (IAS16, 36): A Comparative Study of the State Company for Travelers and delegates Transportations
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The Accounting Disclosure for non-current intangible assets is necessary to rely on accounting information by decision makers in the economic unity, two international accounting standards issued (IAS16,36), which aims to provide the foundations of the recognition, measurement and disclosure of appropriate assets Non-current tangible. (IAS16) allowed to use re-evaluation approach to measure assets entrance due to the inadequacy of the accounting information resulting from the application of the historical cost of the entrance under increasing technical developments and continuing that leave clear their effects on non-current intangible assets, As well as the requirements of what came (IAS36) the importance of accounting for the impairment

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Publication Date
Wed Jan 01 2014
Journal Name
Scienceasia
A combined compact genetic algorithm and local search method for optimizing the ARMA(1,1) model of a likelihood estimator
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In this paper, a compact genetic algorithm (CGA) is enhanced by integrating its selection strategy with a steepest descent algorithm (SDA) as a local search method to give I-CGA-SDA. This system is an attempt to avoid the large CPU time and computational complexity of the standard genetic algorithm. Here, CGA dramatically reduces the number of bits required to store the population and has a faster convergence. Consequently, this integrated system is used to optimize the maximum likelihood function lnL(φ1, θ1) of the mixed model. Simulation results based on MSE were compared with those obtained from the SDA and showed that the hybrid genetic algorithm (HGA) and I-CGA-SDA can give a good estimator of (φ1, θ1) for the ARMA(1,1) model. Anot

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Publication Date
Thu Dec 15 2022
Journal Name
Al-academy
The art of adornment and make-up in the ancient civilizations of Mesopotamia and the old country of Yemen as a model
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This research sheds light on those discrepancies in the use of ornaments, adornment and perfumes, as well as the art of cosmetics, in two important civilizations, namely, the Mesopotamian civilization as the earlier civilization, and the civilization of Yemen, which represents the first Arab civilization. Through the foregoing, our research includes two topics, the first topic included the history of the use of decorations, ornaments and perfumes in the civilization of Mesopotamia, while the second topic included the study of ornaments, adornment and cosmetic art in the ancient civilization of Yemen. And then the research came out with a number of conclusions that the researcher considers very important to highlight the differences and f

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Publication Date
Mon Nov 02 2020
Journal Name
International Journal Of Pharmaceutical Research
Serum Afamin As A Novel Biomarker for Non-Alcoholic Fatty Liver Disease as A Complication of Hypothyroidism in Iraqi Patients.
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Publication Date
Wed Mar 18 2020
Journal Name
Baghdad Science Journal
The A Comparative Study of the Adsorption of Crystal Violet Dye from Aqueous Solution on Rice Husk and Charcoal
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n this work, the adsorption of crystal violet dye from aqueous solution on charcoal and rice husk has been investigated, where the impact of variable factors (contact time; the dosage of adsorbent, pH, temperature, and ionic strength) have been studied. It has been found that charcoal and rice husk have an appropriate adsorption limit with regards to the expulsion of crystal violet dye from fluid arrangements. The harmony adsorption is for all intents and purposes accomplished in 45 min for charcoal and 60 min for rice husk. The amount of crystal violet dye adsorbed (0.4 g of charcoal and 0.5 g of rice husk) increased with an increasing pH and the value of 11 is the best. The effect of temperature on the adsorption process was studied

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Publication Date
Wed Mar 18 2020
Journal Name
Baghdad Science Journal
The A Comparative Study of the Adsorption of Crystal Violet Dye from Aqueous Solution on Rice Husk and Charcoal
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            In this work, the adsorption of crystal violet dye from aqueous solution on charcoal and rice husk has been investigated, where the impact of variable factors (contact time; the dosage of adsorbent, pH, temperature, and ionic strength) have been studied. It has been found that charcoal and rice husk have an appropriate adsorption limit with regards to the expulsion of crystal violet dye from fluid arrangements. The harmony adsorption is for all intents and purposes accomplished in 45 min for charcoal and 60 min for rice husk. The amount of crystal violet dye adsorbed (0.4 g of charcoal and 0.5 g of rice husk) increased with an increasing pH and the value of 11 is the best

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Publication Date
Wed Feb 12 2020
Journal Name
Journal Of Xi'an University Of Architecture & Technology
A COMPARATIVE STUDY OF DIRECTIVES IN SAMUEL BECKETT’S ‘END GAME’ AND ‘WAITING FOR GODOT’
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DBN Rashid, JOURNAL OF XI'AN UNIVERSITY OF ARCHITECTURE & TECHNOLOGY, 2020

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