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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 Mar 24 2009
Journal Name
كتاب الوقائع /المؤتمر العلمي الثالث لكلية العلوم جامعة بغداد
Using antibiotics as mutagenic and curing agents for Prodigiosin Production By Serratia marcescens
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The effect of different antibiotics on growth pigment and plasmid curing of Serratia marcescens were studied, S. marcescens was cultured in media containing(16_500)µg/ml of antibiotics, curing mutants unable to produce prodigiosin and lost one plasmid band were obtained of of ampicillin, amoxillin, antibiotics concentrations (64 500) µg/ml metheprim, ultracloxam, azithromycin, cephalexin and erythromycin treated with (350 500) µg/ml of The mutant cells rose- light color and and refampicin revealed S.marcescens inhibited ciprodar and tetracyclin, lincomycin did not lost the plasmid band chlaforan

Publication Date
Wed Sep 30 2015
Journal Name
Journal Of Natural Sciences Research
Study the levels of GPCR, GLP-1 and related hormones controlled and uncontrolled in diabetic patient's.
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The aim of the present study is to evaluate the change in the levels of glucagon, GLP-1 and GPCR in diabetic patient's and diabetic with dyslipidemia as metabolic syndrome. The study included 75 male aged ranged (30-50) years and with BMI (25-29) kg/m2 which divided into three groups as follows: group one (G1): consist of 25 subjects as healthy control group. Group two (G2): consist of 25 patient's with diabetes mellitus and group three (G3): consist of 25 patient's with diabetic and dyslipidemia as metabolic syndrome. Serum was used in determination of FBG, lipid profile, insulin, glucagon, GLP-1 and GPCR. Whole blood was determination of HbA1c. The results revealed significant elevation in FBG and HbA1c in G2 and G3 comparing to G1. While

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Publication Date
Sat Sep 28 2024
Journal Name
Asia-pacific Journal Of Molecular Biology And Biotechnology
A novel method for the degradation of human blood clot by immobilised bromelain using multi-walled carbon nanotube and polyphenol oxidase
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Pathological blood clot in blood vessels, which often leads to cardiovascular diseases, are one of the most common causes of death in humans. Therefore, enzymatic therapy to degrade blood clots is vital. To achieve this goal, bromelain was immobilized and used for the biodegradation of blood clots. Bromelain was extracted from the pineapple fruit pulp (Ananas comosus) and purified by ion exchange chromatography after precipitation with ammonium sulphate (0-80 %), resulting in a yield of 70%, purification fold of 1.42, and a specific activity of 1175 U/mg. Bromelain was covalently immobilized on functionalized multi-walled carbon nanotubes (MWCNT), with an enzyme loading of 71.35%. The results of the characterization of free and immobilized

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Publication Date
Fri Jun 20 2025
Journal Name
Bulletin Of The Iraq Natural History Museum
A NEW RECORD OF TWO NEMATODES, MESORHABDITISFRANSENI FUCHS, 1933 (MESORHABDITIDAE) AND PRATYLENCHUSGOODEYI SHER AND ALLEN, 1953 (PRATYLENCHIDAE) WITH MOLECULAR DESCRIPTION FROM IRAQ
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rhabditid Mesorhabditis franseni Fuchs, 1933 (Family, Mesorhabditidae) and pratylenchid nematode Pratylenchus goodeyi Sher and Allen, 1953 (Family, Pratylenchidae). They were illustrated by molecular aspects. All specimens of both genera were cultured and reproduced for DNA extraction. M. franseni (IRQ.ZAh2 PP528819.1 isolate) was characterized. P. goodeyi (IRQ.ZAh5 PP535537 isolate) was also characterized. Selected specimens of these two species were molecularly characterized using the partial ITS-rRNA gene sequences. The ITS-rRNA sequence of IRQ.ZAh2 PP528819.1 isolate had a range of (98.62%-100%) sequence homology with ITS-rRNA sequence of M. franseni available in NCBI database. While, the ITS-rRNA sequence of IRQ.ZAh5 PP535537 isolate h

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Publication Date
Thu Oct 18 2018
Journal Name
Al–bahith Al–a'alami
Watching Cultural Programs in Satellites Channels tv and Its relation to the actual reading of the book
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The research is based on an important subject according to the researchers' estimations. It is the disclosure of the nature of the relationship between Watching to cultural programs in satellite channels and the book's vision of the intellectual, and the pursuit of purchasing and acquiring it It is a scientific addition to the scientific research media because it deals in the field of new about the nature of the relationship between satellite programs and writers, and it provides a scientific development on the importance of satellite channels in the promotion of the book and sales of intellectual elite. The study examined the audience of the recipients of literature for cultural programs, the nature of the public, characteristic

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Publication Date
Wed Jul 01 2020
Journal Name
International Journal Of Pharmaceutical Research
Synthesis, Design, Docking and biological activity of new benzo hydrazide derivatives.
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Publication Date
Sun Mar 01 2020
Journal Name
Iop Conference Series: Materials Science And Engineering
Evolution and set up the maps for solar radiation of Iraq using Data observation and Angstrom model during monthly July2017
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Abstract<p>The development that solar energy will have in the next years needs a reliable estimation of available solar energy resources. Several empirical models have been developed to calculate global solar radiation using various parameters such as extraterrestrial radiation, sunshine hours, albedo, maximum temperature, mean temperature, soil temperature, relative humidity, cloudiness, evaporation, total perceptible water, number of rainy days, and altitude and latitude. In present work i) First part has been calculated solar radiation from the daily values of the hours of sun duration using Angstrom model over the Iraq for at July 2017. The second part has been mapping the distribution of so</p> ... Show More
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Publication Date
Thu Sep 01 2011
Journal Name
Journal Of Economics And Administrative Sciences
Determination Of The Efficient Production Plans For Al-Shaheed Public Company By Using Tatget Motad Model Under Risk And Uncertainty
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The research aims to derive the efficient industrial plans for Al – shaheed public company under risk by using Target MOTAD as a linear alternative  model for the quadratic programming models.

The results showed that there had been a sort of (trade- off) between risk and the expected gross margins. And if the studied company strives to get high gross margin, it should tolerate risk and vice versa. So the management  of Al- Shaheed Company to be invited to apply the suitable procedures in the production process, in order to get efficient plans that improves it's  performance .

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Publication Date
Sat Mar 30 2024
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Optimization of Separator Size and Operating Pressure for Three-phase Separators in the West Qurna1 Oil Field
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An optimization study was conducted to determine the optimal operating pressure for the oil and gas separation vessels in the West Qurna 1 oil field. The ASPEN HYSYS software was employed as an effective tool to analyze the optimal pressure for the second and third-stage separators while maintaining a constant operating pressure for the first stage. The analysis involved 10 cases for each separation stage, revealing that the operating pressure of 3.0 Kg/cm2 and 0.7 Kg/cm2 for the second and third stages, respectively, yielded the optimum oil recovery to the flow tank. These pressure set points were selected based on serval factors including API gravity, oil formation volume factor, and gas-oil ratio from the flow tank.    To impro

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Publication Date
Sun Sep 30 2012
Journal Name
College Of Islamic Sciences
Surat Al-Qaria: a linguistic study
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Praise be to God, Lord of the worlds, and the best of prayers, and extradition was made to our master Muhammad and his whole family and companions:
And after:
Surat Al-Qariah is from the royal fence, which is in the thirtieth part of the Noble Qur’an. The commentators differed on the number of verses, and the reason for its naming. This surah talked about the conditions of people on the Day of Resurrection, and about how people were removed from their graves, all of which I spoke about in the preamble.
The research is divided into six topics: the first topic dealt with strange terms, while the second topic dealt with the most important audio issues mentioned in the surah, namely (slurring, advertising, substitution, and silenc

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