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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 Oct 01 2019
Journal Name
International Journal Of Pharmaceutical Research
Study of aminoacy lt ran-synthetasecomplex interacting multifunctional protein 1 and liver enzymes in iraqi women with breast cancer undergoing chemotherapy
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Breast carcinoma is one of the greatest popular neoplasms in females. It is a major reason of demise in the world, and it is the first cancer in ranking diagnosed in Iraqi women. This study aimed to determine aminoacyltRAN-synthetase complex interacting multifunctional protein 1 and liver enzymes levels in Iraqi females with stage II breast malignance, and study the effect of chemotherapy (after surgery) on these markers. This study included 50 females patients with stage II breast malignance (before and after surgery and second dose of chemotherapy) attending the Oncology Teaching Hospital in Medical City/ Baghdad, in addition to 20 persons as controller group were chosen without any chronic diseases. Their ages ranged from (30-55) years.

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Publication Date
Sun Dec 01 2013
Journal Name
Baghdad Science Journal
Theoretical Study of Charge Transfer in Styryl Thiazilo Quinoxaline Dyes STQ-1, STQ-2,and STQ-3 in Organic Media System
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Charge transfer in styryl dyes STQ-1, STQ-2,and STQ-3 with organic media system has been studied theoretically depending on the Franck- Condon rule and continuum dielectric model . The reorientation energies (eV) were evaluated theoretically depending on dipole momentum, dielectric constant , and refrective index n. The rate constant of charge transfer has been calculated depending on the reorientation energy (eV) ,effective free energy , potential height barrier , and coupling coefficient . A matlap program has been written to calculated the rate constant of charge transfer and other parameter. The results of calculations show that STQ-2 dye is more reaction for charge transfer compare with STQ-1 and STQ-3 dyes

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Publication Date
Sun Apr 08 2018
Journal Name
Al-khwarizmi Engineering Journal
Kinetic Study of the Leaching of Iraqi Akashat Phosphate Ore Using Lactic Acid
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     In the present work, a kinetic study was performed to the extraction of phosphate from Iraqi Akashat phosphate ore using organic acid. Leaching was studied using lactic acid for the separation of calcareous materials (mainly calcite). Reaction conditions were 2% by weight acid concentration and 5ml/gm of acid volume to ore weight ratio. Reaction time was taken in the range 2 to 30 minutes (step 2 minutes) to determine the reaction rate constant k based on the change in calcite concentration. To determine value of activation energy when reaction temperature is varied from 25 to 65 , another investigation was accomplished. Through the kinetic data, it was found that selective leaching was controlled by surface chemical reactio

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Publication Date
Sun Apr 08 2018
Journal Name
Al-khwarizmi Engineering Journal
Kinetic Study of the Leaching of Iraqi Akashat Phosphate Ore Using Lactic Acid
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     In the present work, a kinetic study was performed to the extraction of phosphate from Iraqi Akashat phosphate ore using organic acid. Leaching was studied using lactic acid for the separation of calcareous materials (mainly calcite). Reaction conditions were 2% by weight acid concentration and 5ml/gm of acid volume to ore weight ratio. Reaction time was taken in the range 2 to 30 minutes (step 2 minutes) to determine the reaction rate constant k based on the change in calcite concentration. To determine value of activation energy when reaction temperature is varied from 25 to 65 , another investigation was accomplished. Through the kinetic data, it was found that selective leaching was controlled by

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Publication Date
Wed Oct 01 2014
Journal Name
Al–bahith Al–a'alami
The electronic news bulletin of the ministry of higher education and scientific research: A study in the newspapers of: (AL-Taakhi, AL-Zaman, ALAdala,AL-Sabah and Baghdad) for period from 2nd October 2011 to 1st November 2011
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The research aims to know the reverberation of the the electronica news bulletin of the ministry of higher education and scientific research  in the newspapers of: (AL-Taakhi, AL-Zaman, ALAdala,AL-Sabah and Baghdad) for period from 2nd October 2011 to 1st November 2011 to explain its activity and advantage for the other newspapers and to show the importance which the newspapers showed for the study of the news subject in the bulletin, as well as,to show the proportional differences in which the newspapers interested in the subjects of the published news, and to reach to the results which lead us to good conclusions for the service of decision owner and open new horizons for the researchers to expanding in the s

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Publication Date
Tue Jun 30 2015
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Improving Treatment Performance of Dissolved Air Flotation System by Using Ionic Liquids as Surfactants
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The effect of three ionic liquids viz., 1-hexyl-3-methylimidazolium tetrafluoroborate (ILE), 1-hexyl-3-metylimidazolium hexafluorophosphate (ILF) and 1-octyl-3-methylimidazolium tetrafluoroborate (ILG) when used as surfactants on the performance of dissolved air floatation (DAF) was investigated.

   Experiments were conducted at a temperature of 30-35 ºC, 10ppm ferric chloride as coagulant, 50% recycle ratio, pH 8, and 10 minutes treatment time  to find oil and grease (OG) and turbidity removal efficiencies at saturation pressure (2-6) bar.

ILs were used at concentration of 50 µl/liter of treated water in two positions in DAF system; the saturation vessel and the treatment tank. The performance using ILs

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Publication Date
Tue Jul 30 2019
Journal Name
Sn Applied Sciences
Removal of oil emulsion from aqueous solution by using Ricinus communis leaves as adsorbent
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Publication Date
Tue Jan 01 2013
Journal Name
International Journal Of Advances In Pharmacy, Biology And Chemistry
Synthesis of NSAID with Sulfonamide Conjugates as Possible Mutual Prodrugs using Amino Acid Spacer
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The purpose of this research work is to synthesize conjugates of NSAIDs (ibuprofen, and naproxen) with sulfadiazine as possible mutual prodrugs to overcome the local gastric irritation of NSAIDs with free carboxyl group by formation of ester linkage that supposed to remain intact in stomach and may hydrolyze in intestine chemically or enzymatically; in addition to that attempting to target the synthesized derivative to the colon by formation of azo bond that undergo reduction only by colonic bacterial azoreductaze enzyme to liberate the parent compound to act locally (treatment of inflammation and infections in colon)

Publication Date
Wed Oct 11 2023
Journal Name
Journal Of Educational And Psychological Researches
Motivations of Volunteers in Jordan: An Exploratory Study Based on a Sample of University Students within the Context of their Social Relations
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Volunteerism is an element included in many human cultures. It represents a positive cooperative act between individuals and groups. It expresses the social value systems. As a social phenomenon, it develops in societies according to innumerous circumstances and conditions. This study uses a functional approach that assumes that volunteering performs six functions for volunteers. Namely, we assume that volunteering (1) creates a sense of protection (2) meets significant cultural values (3) improves professional status of volunteers, (4) strengthens their social relationships, (5) helps them achieve a better understanding of life, and finally, (6) enhances their outlook and self-esteem. The central aim of the study is to discuss these fun

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Publication Date
Tue Mar 19 2024
Journal Name
Jordan Journal Of Pharmaceutical Sciences
MMP-1 and MMP-7 Expression is Influenced by Ginsenosides in Mice Exposed to Aflatoxin B1: in vivo Study
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Panax ginseng (PG), one of the most widely used herbal medicines, has demonstrated various beneficial effects such as anti-inflammatory, antioxidant, and anticancer impacts. Naturally occurring ginsenosides in the ginseng plant inhibit cell proliferation and significantly reduce liver damage induced by certain chemicals. Aflatoxin B1 (AFB1) is a primary mycotoxin due to its hepatotoxic, immunotoxic, and oncogenic effects in animal models and humans. In this study, we examined the effects of assorted doses of PG aqueous crude extract on the expression of matrix metalloproteinase 1 and 7 (MMP-1 and MMP-7) in the kidney, spleen, and liver of experimental AFB1-exposed mice, using immunohistochemistry (IHC). Mice were orally administered

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