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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
Wed Oct 09 2019
Journal Name
Journal Of The College Of Education For Women
Naber and toning in the modern Arab poetry Mahmoud Darwish, a model
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Naber and toning in the modern Arab poetry Mahmoud Darwish, a model

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Publication Date
Sun Dec 30 2012
Journal Name
College Of Islamic Sciences
A study of the hadiths of supplication orchestration
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A study of the hadiths of supplication orchestration

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Publication Date
Wed Nov 01 2023
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Preparation and characterization of Posaconazole as a Nano-micelles using d-α-Tocopheryl polyethylene glycol 1000 succinate (TPGS)
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It is important to note that Posaconazole (POCZ) is a newly developed extended-spectrum triazole that belongs to BCS class II and has a solubility of less than 1µg/ml. In patients with a weakened immune system, POCZ has been shown to be effective as an antifungal treatment for invasive infections caused by candida and aspergillus species. The nano-micelles technique can be used to increase POCZ solubility. In order to increase their apparent solubility in water, nano-micelles are made by combining macromolecules that self-assemble into ordered structures capable of entrapping hydrophobic drug molecules in the interior domain. Dispersed colloidal systems, of which nano-micelles are a subset, are a large and diverse group. Composed of a p

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Publication Date
Tue Jan 12 2021
Journal Name
Pollution Research
DETERMINATION OF ANILINE IN WASTEWATER BY CLOUDPOINT EXTRACTION FOLLOWED BY HPLC USING 8-HYDROXYQUINOLINE AS A DERIVATIZATION AGENT
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A procedure, depending on the derivatization and determination of aniline was depicted andvalidated in this study. 8-hydroxyquinoline (8-HQ) was used as the derivatizing agent for thedetermination of aniline. An optimization study was performed for the derivatization reaction, i.e.,the diazonium coupling reaction, the optimum parameters were as follows: 22 mM of hydrochloricacid, 54mM of sodium hydroxide, and 1.8mM of sodium nitrate. The optimization study of themethod of cloud point extraction (CPE) revealed that the extraction solvent was 0.5 ml of Triton X-100, the optimum temperature was 90 °C, and the incubation time was 25 min. The linearity,correlation coefficients, molar absorptivities, and limits of detection were improved using t

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Publication Date
Wed Oct 31 2018
Journal Name
Heat Transfer-asian Research
Comparative study on heat transfer enhancement of nanofluids flow in ribs tube using CFD simulation
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Publication Date
Sat Apr 01 2023
Journal Name
Journal Of Engineering
Comparative Study of Water Desalination using Reverse Osmosis (RO) and Electro-dialysis Systems (ED): Review
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The increasing drinking water demand in many countries leads to an increase in the use of desalination plants, which are considered a great solution for water treatment processes. Reverse osmosis (RO) and electro-dialysis (ED) systems are the most popular membrane processes used to desalinate water at high salinity. Both systems work by separating the ionic contaminates and disposing of them as a brine solution, but ED uses electrical current as a driving force while RO uses osmotic pressure. A direct comparison of reverse osmosis and electro-dialysis systems is needed to highlight process development similarities and variances. This work aims to provide an overview of previous studies on reverse osmosis and electro-dial

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Publication Date
Thu Jan 23 2020
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Loss Reduction and prevention programs
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The risks are considered as a large challenge facing the human communities. This challenge creates an economic and social burden which obstruct the community progress and influences on its evaluation in a negative way. In the last years, these risks began to increase and now it is necessary to face these risks in a regular and instructive methods in order to control over these risks and to limit its effects and reducing the losses, if it happened. The loss reduction and prevention programs produced by risks management are considered as a successful solution which enable to control these risks. These programs would not finish the danger in the community in a final way but it produces a practical solution reduces the negative effects and c

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Publication Date
Thu Dec 01 2022
Journal Name
Baghdad Science Journal
Molecular Characterization of Potential Crop Pathogens Associated with Weeds as Endophytes in Uniilorin Plantations, Nigeria
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Crop diseases are usually caused by inoculum of pathogens which might exist on alternate hosts or weeds as endophytes. These endophytes, cum pathogens, usually confer some beneficial attributes to these weeds or alternate hosts from protection against herbivores, disease resistance, stress tolerance to secondary metabolites production. This study was therefore carried out to isolate potential crop pathogens which exist as endophytes on weed species in the University of Ilorin plantations. Green asymptomatic leaves were collected from 10 weed species across the plantations, and processed for their endophytic fungi isolation. Isolates were purified into pure cultures and used for molecular identification using the internal transcribed spac

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Publication Date
Wed Mar 10 2021
Journal Name
Baghdad Science Journal
A study of some atomic properties for He-like selected ions
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The atomic properties have been studied for He-like ions (He atom, Li+, Be2+ and B3+ions). These properties included, the atomic form factor f(S), electron density at the nucleus , nuclear magnetic shielding constant and diamagnetic susceptibility ,which are very important in the study of physical properties of the atoms and ions. For these purpose two types of the wave functions applied are used, the Hartree-Fock (HF) waves function (uncorrelated) and the Configuration interaction (CI) wave function (correlated). All the results and the behaviors obtained in this work have been discussed, interpreted and compared with those previously obtained.

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Publication Date
Sun Feb 03 2019
Journal Name
Journal Of The College Of Education For Women
A Factorial Study for separation anxiety in students, of Baghdad City
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A Factorial Study for separation anxiety in students, of Baghdad City

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