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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 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 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
Mon Jul 04 2016
Journal Name
University Of Plymouth
‘History Engraved on his Shoulder’: A Comparative Study of the Influence of British First World War Poetry on Post 1980 Iraqi War Poetry "embargoed indefinitely"
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Abstract This study aims to compare British war poetry of the First World War with Iraqi poetry from the mid-20th century with special reference to Iraqi war poetry of the 1980’s Iraq-Iran War and the period that followed it. It will also investigate the influence of the designated British war poetry on the chosen body of Iraqi poetry. Through the comparison of sample poems the study presents, firstly, the direct influence of the British poetry of the Great War and its translation which formed the seeds of a more radical movement in Iraqi poetry during the 1980’s Iran/Iraq War and the period that followed it. The study also presents a comparison of the works of British and Iraqi civilian poets during and after the war time and their con

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Publication Date
Sun Dec 02 2012
Journal Name
Baghdad Science Journal
Study of Spectroscopy and Thermodynamic Properties for Phoshours dioxide PO2 Molecular and Influence Study of Bond ( P-O ) on Spectroscopy Properties
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In This research a Spectroscopic complement and Thermodynamic properties for molecule PO2 were studied . That included a calculation of potential energy . From the curve of total energy for molecule at equilibrium distance , for bond (P-O), the degenerated of bond energy was (4.332eV) instate of the vibration modes of ( PO2 ) molecule and frequency that was found active in IR spectra because variable inpolarization and dipole moment for molecule. Also we calculate some thermodynamic parameters of ( PO2 ) such as heat of formation , enthalpy , heat Of capacity , entropy and gibb's free energy Were ( -54.16 kcal/mol , 2366.45 kcal/mol , 10.06 kcal /k/mol , 59.52 k

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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
Sat Aug 01 2020
Journal Name
Key Engineering Materials
Compressive Strength Performance of Reactive Powder Concrete Using Different Types of Materials as a Partial Replacement of Fine Aggregate
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Reactive Powder Concrete (RPC) can be incorporate as a one of the most important and progressive concrete technology. It is a special type of ultra-high strength concrete (UHSC) that’s exclude the coarse aggregate from its constitutive materials. In this research an experimental study had been carried out to investigate the effect of using three types of materials (porcelain aggregate) and others sustainable materials (glass waste and granular activated carbon) as a partial replacement of fine aggregate. Four percentages had considered (0, 10, 15 and 20) % to achieve better understanding for the influence of these materials upon the compressive strength of RPC. Four curing ages had included in this study, these are; 7, 28, 60 and

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Publication Date
Sat Aug 01 2020
Journal Name
Key Engineering Materials
Compressive Strength Performance of Reactive Powder Concrete Using Different Types of Materials as a Partial Replacement of Fine Aggregate
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Reactive Powder Concrete (RPC) can be incorporate as a one of the most important and progressive concrete technology. It is a special type of ultra-high strength concrete (UHSC) that’s exclude the coarse aggregate from its constitutive materials. In this research an experimental study had been carried out to investigate the effect of using three types of materials (porcelain aggregate) and others sustainable materials (glass waste and granular activated carbon) as a partial replacement of fine aggregate. Four percentages had considered (0, 10, 15 and 20) % to achieve better understanding for the influence of these materials upon the compressive strength of RPC. Four curing ages had included in this study, these are; 7, 28, 60 and

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Publication Date
Thu Aug 21 2025
Journal Name
Journal Of Physical Education
A comparative analysis , for some Elkinmetekih variables , in the performance of the skill (Nick shot the front reverse ) , between the players of the Iraqi team and the Egyptian , for young people in squash
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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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