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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 Oct 01 2022
Journal Name
Advances In Structural Engineering
Experimental and FE analysis of composite RC beams with encased pultruded GFRP I-beam under static loads
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Publication Date
Mon Jul 01 2019
Journal Name
Reviews In Medical Microbiology
Expression of virulence and antimicrobial resistance genes among Escherichia coli clinical isolates from blood and stool samples
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Objective:

As major nosocomial pathogens, Escherichia coli isolates exhibit antibiotic resistance and also express adhesive structures and antibiotic resistance genes. The objective of this study was the comparison of virulence gene expression of extended-spectrum beta-lactamase (ESBL)-producing E. coli between blood and stool samples.

Methods:

In this study, 20 E. coli clinical isolates (10 ESBL-producers including 5 from blood, 5 from stool sample

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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)
Possible Anti-Asthmatic Effect of Iraqi Ammi Majus Seeds Extract Against Asthma Induced by Ovalbumin in Mice
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Asthma is a chronic respiratory disorder of airways characterized by inflammation, hyperresponsiveness, inflammatory cell infiltration, mucous secretion, and remodelling. Ammi majus is medicinal plant belong to family of Apiaceous which has anti-inflammatory and antioxidant activities. This study designed to investigate of anti-asthmatic activity of alcoholic extract of Ammi majus in improvement of asthma. Forty-eight healthy female mice divided to six groups Group I:  the negative control group (distal water only), Group II: Positive control group (ovalbumin group), Group III: Ammi majus (64 mg/kg/day) with sensitization, Group IV:Ammi majus  (128 mg/kg/day) with sensitization, Group V: Ammi majus (64 mg/kg/day) without sensitiza

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Publication Date
Mon Dec 21 2020
Journal Name
Bulletin Of The Iraq Natural History Museum (p-issn: 1017-8678 , E-issn: 2311-9799)
SEASONAL FLUCTUATION OF STINK BUG MUSTHA SPINULOSA (LEFEBVRE, 1831) (HEMIPTERA, PENTATOMIDAE) ON SOME TREES IN ERBIL CITY
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Phytophagous stink bugs (Hemiptera, Pentatomidae) are economically important insect pests of fruit, vegetable, nut and field crops. This study was carried out during the season of 2013 in orchards within Erbil city, to follow the stink bug Mustha spinulosa (Lefebvre, 1831) seasonal fluctuation on some fruit trees: olive, plum, apricot, pear, apple and almond.
The stink bug reaches its maximum abundance throughout the second week of August (38.2/tree) coinciding with mean temperature and relative humidity of 33.40C and 28.14% respectively, and the highest total mean of the number of the insect was recorded on the olive trees (181.8/tree). The study reveals that the stink bug attacked 22 trees (fruit and forest) while it has not atta

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Publication Date
Mon Apr 23 2018
Journal Name
International Journal Of Quantum Information
Key rate estimation of measurement-device-independent quantum key distribution protocol in satellite-earth and intersatellite links
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In this work, an estimation of the key rate of measurement-device-independent quantum key distribution (MDI-QKD) protocol in free space was performed. The examined free space links included satellite-earth downlink, uplink and intersatellite link. Various attenuation effects were considered such as diffraction, atmosphere, turbulence and the efficiency of the detection system. Two cases were tested: asymptotic case with infinite number of decoy states and one-decoy state case. The estimated key rate showed the possibility of applying MDI-QKD in earth-satellite and intersatellite links, offering longer single link distance to be covered.

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Publication Date
Sat Apr 25 2020
Journal Name
Indian Journal Of Forensic Medicine & Toxicology
Flame Atomic Absorption Spectrophotometry Analysis of Heavy Metals in Some Food Additives Available in Baghdad Markets, Iraq
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Publication Date
Wed Oct 21 2020
Journal Name
British Journal Of Cancer
Epigenome-wide analysis reveals functional modulators of drug sensitivity and post-treatment survival in chronic lymphocytic leukaemia
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Abstract<sec> <title>Background

Chronic lymphocytic leukaemia (CLL) patients display a highly variable clinical course, with progressive acquisition of drug resistance. We sought to identify aberrant epigenetic traits that are enriched following exposure to treatment that could impact patient response to therapy.

Methods

Epigenome-wide analysis of DNA methylation was performed for 20 patients at two timepoints during treatment. The prognostic significance of differentially methylated regions (DMRs) was assessed in independent cohorts of 139 and 1

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Publication Date
Wed Dec 01 2010
Journal Name
Iraqi Journal Of Physics
Current–voltage and capacitance-voltage characteristics of Se/Si heterojunction prepared by DC planar magnetron sputtering technique
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In this work, the effect of annealing temperature on the electrical properties are studied of p-Se/ n-Si solar cell, which p-Se are deposit by DC planar magnetron sputtering technique on crystal silicon. The chamber was pumped down to 2×10−5 mbar before admitting the gas in. The gas was Ar. The sputtering pressure varied within the range of 4x10-1 - 8x10-2mbar by adjusting the pumping speed through the opening control of throttle valve. The electrical properties are included the C-V and I-V measurements. From C-V measurements, the Vbi are calculated while from I-V measurements, the efficiency of solar cell is calculated.

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Publication Date
Wed Feb 01 2023
Journal Name
South African Journal Of Botany
Ability of FeNi3/SiO2/TiO2 nanocomposite to degrade amoxicillin in wastewater samples in solar light-driven processes
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Publication Date
Tue Dec 20 2022
Journal Name
Bulletin Of The Iraq Natural History Museum (p-issn: 1017-8678 , E-issn: 2311-9799)
DISTRIBUTION AND PHYLOGENETIC OF FRESHWATER MUSSEL UNIO TIGRIDIS BOURGUIGNAT, 1852 (BIVALVIA, UNIONIDAE) FROM GREATER ZAB RIVER, IRAQ
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Freshwater mussels are a guild of stationary, suspended-feeding species; they perform significant ecological functions like nitrogen cycling, bioturbation that gives oxygen and habitat that other creatures need to survive, and increasing water clearance by filtration. Knowledge of the freshwater mussel Unio tigridis Bourguignat, 1852, distribution, and molecular study in Iraq was inadequate. In the current study, this species of freshwater Mussels belonging to the family Unionidae was collected from different locations in the Greater Zab River, from April 2022 to November 2022. The average water temperature of the site was arranged between (17.8 to 36.1 C°). All previous studies in the Kurdistan Region and Iraq were based on morphologic

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