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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
Sun Mar 17 2019
Journal Name
Baghdad Science Journal
The Potential of some Plant Extracts as Radical Scavengers and Dipeptidyl Peptidase-4 Inhibitors
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Seeds, beans, leaves, fruit peel and seeds of five plants (Ferula assa-foetida, Coffea robusta, Olea europaea, Punica granatum and Vitis vinifera, respectively) were extracted with four solvents (distilled water, 80% methanol, 80% acetone and a mixed solvent that included methanol, ethanol, acetone and n-butanol at proportions 7:1:1:1). Such manipulation yielded 20 extracts, which were phytochemically analyzed for total polyphenols (TP) and flavonoids (TF). The DPPH (2,2-diphenyl-1-picrylhydrazyl) radical scavenging activity (RSA) and DPP-4 (dipeptidyl peptidase-4) relative inhibition activity (RIA) were also assessed for each extract. The results revealed that mixed solvent extract of V.

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Publication Date
Fri Feb 01 2019
Journal Name
Journal Of Economics And Administrative Sciences
A Comparison of Parameters Estimation Methods for the Negative Binomial Regression Model under Multicollinearity Problem by Using Simulation
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This study discussed a biased estimator of the Negative Binomial Regression model known as (Liu Estimator), This estimate was used to reduce variance and overcome the problem Multicollinearity between explanatory variables, Some estimates were used such as Ridge Regression and Maximum Likelihood Estimators, This research aims at the theoretical comparisons between the new estimator (Liu Estimator) and the estimators

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Publication Date
Tue Dec 12 2017
Journal Name
Al-khwarizmi Engineering Journal
Design a Vegetative Filter Strips Length Using VFSMOD_W Model for Reducing Sediments and Pesticides
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 Abstract 

The vegetative filter strips (VFS) are a useful tool used for reducing the movement of sediment and pesticide in therivers. The filter strip’s soil can help in reducing the runoff volume by infiltration. However, the characteristics of VFS (i.e., length) are not recently identified depending on the estimation of VFS modeling performance. The aim of this research is to study these characteristics and determine acorrelation between filter strip length and percent reduction (trapping efficiency) for sediment, water, and pesticide. Two proposed pesticides(one has organic carbon sorption coefficient, Koc, of 147 L/kg which is more moveable than XXXX, and another one

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Publication Date
Fri Jan 01 2016
Journal Name
Journal Of Engineering
A Mathematical Model of a Thermally Activated Roof (TAR) Cooling System Using a Simplified RC-Thermal Model with Time Dependent Supply Water Temperature
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This paper presents a computer simulation model of a thermally activated roof (TAR) to cool a room using cool water from a wet cooling tower. Modeling was achieved using a simplified 1-D resistance-capacitance thermal network (RC model) for an infinite slab. Heat transfer from the cooling pipe network was treated as 2-D heat flow. Only a limited number of nodes were required to obtain reliable results. The use of 6th order RC-thermal model produced a set of ordinary differential equations that were solved using MATLAB - R2012a. The computer program was written to cover all possible initial conditions, material properties, TAR system geometry and hourly solar radiation. The cool water supply was considered time

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Publication Date
Fri Mar 15 2024
Journal Name
Journal Of Baghdad College Of Dentistry
Efficiency of osseodensification versus screw expansion technique for augmentation of narrow alveolar ridges: A comparative clinical study
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Background: Alveolar ridge expansion is proposed when the alveolar crest thickness is ≤5 mm. The screw expansion technique has been utilized for many years to expand narrow alveolar ridges. Recently, the osseodensification technique has been suggested as a reliable technique to expand narrow alveolar ridges with effective width gain and as little surgical operating time as possible. The current study aimed to compare osseodensification and screw expansion in terms of clinical width gain and operating time. Materials and methods: Forty implant osteotomies were performed in deficient horizontal alveolar ridges (3–5 mm). A total of 19 patients aged 21–59 years were randomized into two groups: the screw expansion group, which invo

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Publication Date
Tue Jun 19 2018
Journal Name
Elmofaker Review
The Secondary Liability of Electronic Auctions Arising from Contributory Trademark Infringement – A Comparative Study
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Despite the global economic downturn, online e-commerce, especially the sale of counterfeit goods, continues to witness a rise in sales, and one of the important players in e-commerce is the owners of e-commerce auction sites. Although they do not have a direct role in trademark infringement, they still consider them indirectly responsible (secondary liability) for infringing on their trademarks. Thus, many cases have been filed by the owners of the original trademarks (which have been infringed by persons who have sold some of the goods and products that are imitating their marks through some electronic auctions) against the owners of those auctions. In view of the international character of the Internet, in different countries, and despit

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Publication Date
Sun Dec 28 2025
Journal Name
Al–bahith Al–a'alami
CARTOON SEMIOTIC ABOUT MARCH OF RETURN IN THE PALESTINIAN NEWSPAPERS: : (A Comparative Analytical Study)
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This study aims to reveal the semiotic of “March of Return” cartoon in the Palestinian journalism, topics, Symbols and semantics that were covered.
This study is descriptive. It uses the survey method. Content analysis, and methodological comparison was also used.

The researcher chose an intentional sample of Palestine and Al-Hayat Al-Jadida newspapers for one year from March 30, 2018 to March 31, 2019, through a comprehensive inventory of all cartoons of the return marches during this period, which amounted to 59 cartoons.

The study has reached the following findings:

Newspapers cartoons focused on the topics of durability of the protester

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Publication Date
Mon Apr 01 2019
Journal Name
Journal Of Oral And Maxillofacial Surgery
Pain Reduction in Extensive Apical Surgery of the Anterior Maxilla: A Comparative Clinical Study
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Publication Date
Thu Apr 01 2021
Journal Name
Journal Of Molecular Structure
Mixed-ligand complexes of ampicillin derived Schiff base ligand and Nicotinamide: Synthesis, physico-chemical studies, DFT calculation, antibacterial study and molecular docking analysis
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A novel series of mixed-ligand complexes of the type, [ML1(L2)3]Clx [M= Cr(III), Fe(III), Co(II),Ni(II), Cu(II), Cd(II) and Hg(II), n = 2, 3], was synthesized using Schiff base (HL1) as main ligand, nicotinamide (L2) as secondary ligand, and the corresponding metal ions in 1:3:1 molar ratio. The main ligand, HL1 was prepared by the interaction of ampicillin drug and 4-chlorobenzophenone. The synthesized mixed ligand complexes were characterized by elemental analysis, UV-Vis, FT-IR,1H-NMR,13C-NMR and TG/DTG studies. In the mixed-ligand complexes, the Schiff base ligand, HL1 showed coordination to the central metal ion in tridentate manner via azomethine nitrogen, β-lactam ring oxygen and deprotonated carboxylic oxygen atoms, whereas the sec

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Publication Date
Fri Dec 01 2017
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Determining the Optimal Ratio of Liquidity in Iraqi Commercial Banks for period (2005-2013): applied research using Iraqi Commercial Banks as a sample study
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  This study  focused on a fundamental issue which was represented by ability of Iraqi central bank in facing the difficulty of determining  the optimal ratio of liquidity in the Iraqi banks in terms of the balancing between its obligations to the depositors and borrowers, and liquidate their funds on one hand and the risks on the other hand.the search aimed  for achieving the goals which represented by identifying the possibility of Iraqi banks to apply the regulations rules and  instructions  issued by central bank  of  Iraq in determining  ratio  of  liquidity and  its  appropriate with Iraqi  banks  action to implement  a  reasonable  profit to&

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