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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
Thu Dec 30 2021
Journal Name
Diyala Agricultural Sciences Journal
A Study of Some Biological Aspects of Pacu Piaractus Brachypomus (G. Cuvier, 1818)
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The present study attempts to shed light on some biological aspects and characteristics of Piaractus brachypomus, including some biometrics, phenotypic and feeding pattern that characterizes this species. Besides, the study touches upon the body shape and the Otolith. These fish species have recently been seen frozen in the Iraqi local market. The standard length of fish specimens in this study reach 26.55cm it exceeded the specimens of Pacu fish collected from other studies from other countries, As well the specimens weight was 632gm it exceeded other studies mentioned in this manuscript. As the irregularity in the distribution of teeth rows, especially in the lower jaw was clear in our specimens. The average weight of some skull b

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Publication Date
Wed Mar 15 2023
Journal Name
Journal Of Petroleum Research And Studies
A Numerical Study of Tertiary Oil Recovery by Injection of Low-Salinity Water
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The injection of Low Salinity Water (LSWI) as an Enhanced Oil Recovery (EOR) method has recently attracted a lot of attention. Extensive research has been conducted to investigate and identify the positive effects of LSWI on oil recovery. In order to demonstrate the impact of introducing low salinity water into a reservoir, simulations on the ECLIPSE 100 simulator are being done in this work. To simulate an actual reservoir, an easy static model was made. In order to replicate the effects of injecting low salinity water and normal salinity, or seawater, the reservoir is three-phase with oil, gas, and water. It has one injector and one producer. Five cases were suggested to investigate the effect of low salinity water injection with differen

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Publication Date
Tue Aug 23 2022
Journal Name
Frontiers In Energy Research
Evaluation of T-Shaped Fins With a Novel Layout for Improved Melting in a Triple-Tube Heat Storage System
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The effects of T-shaped fins on the improvement of phase change materials (PCM) melting are numerically investigated in vertical triple-tube storage containment. The PCM is held in the middle pipe of a triple-pipe heat exchanger while the heat transfer fluid flows through the internal and external pipes. The dimension effects of the T-shaped fins on the melting process of the PCM are investigated to determine the optimum case. Results indicate that while using T-shaped fins improves the melting performance of the PCM, the improvement potential is mainly governed by the fin’s body rather than the head. Hence, the proposed T-shaped fin did not noticeably improve melting at the bottom of the PCM domain; additionally, a flat fin is ad

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Publication Date
Sat Apr 01 2023
Journal Name
Siriraj Medical Journal
The Potential of Vitamin-D-Binding Protein as a Urinary Biomarker to Distinguish Steroid-Resistant from Steroid-Sensitive Idiopathic Nephrotic Syndrome in Iraqi Children
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Objective: To determine the ability of uVDBP to discern SRNS from steroid-sensitive nephrotic syndrome (SSNS) in Iraqi children. Materials and Methods: This cross-sectional study enrolled children with SRNS (n=31) and SSNS (n=32) from the pediatric nephrology clinic of Babylon Hospital for Maternity and Pediatrics over three months. Patients' characteristics in terms of demographics, clinical data, and urinary investigations were collected. Quantitative analysis of uVDBP levels was undertaken via a commercially available ELISA kit. Results: The median uVDBP values were significantly higher (p-value<0.001) in the SRNS group (median=10.26, IQR=5.91 μg/mL) than in the SSNS group (median=0.953, IQR=4.12 μg/mL). A negative correlati

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Publication Date
Sat Dec 01 2012
Journal Name
Asian Journal Of Chemistry
Microwave assisted synthesis of new heterocyclic compounds: 1, 2, 3-triazoles and tetrazoles and study of their biological activity
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The work includes synthesis of 1,2,3-triazoles via click conditions and using the microwave irradiation starting from two synthesized azides: 2,3,4,6-tetra-O-acetyl-β-D-glucopyranosyl azide (5) and perfluorobutylethyl azide (10) and different terminal alkynes. It also includes microwave enhanced synthesis of tetrazoles via the reaction of two synthesized azides i.e., perfluorobutylethyl azide (10) and 1,5-diazidopentane (13) with benzoyl cyanide. Most of the prepared compounds have been characterized by: TLC, FT-IR, 1H NMR, 13C NMR, LC-MS and microelemental analysis

Publication Date
Sun Aug 23 2020
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The impact of the capital increase in the rate of return on stock price: Applied in the study of a sample of Iraqi banks
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The capital banking foundation stone upon which the bank in the practice of business activities, the more capital a good financial adequacy of the increased bank's ability to grant credit and expand the various activities and provide a safety element for depositors and other sources of funding to achieve profits and increase the trading volume of the shares, causing the rise the rate of return for the shares of banks and have the Central Bank as head of the banking system by issuing instructions capital increase banking, according to the requirements of economic development and increase gross domestic product by supporting investment projects that are financed through banks, the research aims to show the extent of the banks commitment to

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Publication Date
Thu Oct 17 2024
Journal Name
مجلة ميسان لعلوم التربية البدنية
A historical study of the origins of the sport of polo and its development from the royal court to the stadiums of modern times
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The sport of polo, the game of kings and sultans, is one of the traditional sports that has defied time throughout its long history. It has preserved its historical roots and been able to adapt to contemporary requirements, societal transformations, and temporal and spatial variables. It has moved from an aristocratic sport practiced as a form of entertainment to a professional competitive sport. It attracts many players and millions of viewers, so it is a living model of how sports develop and transform from a local tradition into global sports with organized rules managed by international institutions and with many championships worldwide. Through this, the research objectives were formulated, including exploring sports' origins. Polo in

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Publication Date
Sat Jul 01 2017
Journal Name
Al–bahith Al–a'alami
The Use of Digital Public – Relations in the Work of Iraqi Universities: A Survey Study of the Workers in the Departments of Public Relations
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the digital public relations aim at make the workers getting the necessary information about the governmental institutions where they work and the enveronment surrounding them. it also tries to let the workers get the special knowlege of tthe publich relations and their jobs like the works of planning , arranging the active communication and executive skills needed in their writing , editing , special art skills for designing , production and technological skills to deal with the computer.
the problem of the research includes some questions as :
1- what are the uses achieved by degetal public relations workers at Iraqi universities (Baghdad, Mustansiriya, and Iraqi)
2- what are the tools used to apply digital public relations

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Publication Date
Mon Feb 15 2021
Journal Name
Drug Delivery And Translational Research
Breast intraductal nanoformulations for treating ductal carcinoma in situ II: Dose de-escalation using a slow releasing/slow bioconverting prodrug strategy
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Publication Date
Thu Dec 30 2021
Journal Name
Periodicals Of Engineering And Natural Sciences (pen)
Design a system for an approved video copyright over cloud based on biometric iris and random walk generator using watermark technique
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