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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 Mar 14 2024
Journal Name
Biomedical And Pharmacology Journal
A Summary of the Pharmacological Activity, Phytochemistry and Pharmacognosy of Parthenocissus quinquefolia (L.): A Review
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Historically, medicinal herbs have been utilized as an important origin of chemicals with particular therapeutic potentials, and they continue to be a great place to find new medication candidates. Parthenocissus quinquefolia L. is a member of the grape-growing family Vitaceae. It is indigenous to Central and North America. It is widely dispersed in Iraqi gardens and plant houses from north to south. Traditionally, it has many uses, like relieving constipation, treating jaundice, expectorant, emetic, and others. At the same time, its proven activities include antioxidant activity, antimicrobial, anti-diabetic, thrombin inhibitor effect, and medicine for treating eyelid eczema. Parthenocissus quinquefolia contains valuable phytochemicals lik

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Publication Date
Thu Jan 04 2024
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The Impact of Performance Auditing Process Pursuant to the Programs and Policies Guide in improving the health insurance Prosperity: applied research in the Iraqi General Insurance Company
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Abstract

              The research’s goal lies in demonstrating the impact of the Federal Financial Supervision Endowment through the process of auditing the performance of the entities subject to its audit as to improve the performance of these entities, especially if the performance audit method is one of the newly applied methods that are compatible with the standards issued by the International Organization of Financial Supervision and Accounting Institutions which is the method of auditing performance according to the performance evaluation guide for programs and policies issued by the Federal Office of Financial Supervision.

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Publication Date
Sun Dec 07 2008
Journal Name
Baghdad Science Journal
Three Dimensional MHD Simulationof Comet Hale-Bopp Tail
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The interaction between comet Hale-Bopp tail with the solar wind is investigated in the present paper using magneto-hydrodynamic (MHD) numerical simulation, which accounts for the presence of the interplanetary magnetic field (IMF). The simulation is based on three-dimensional Lax-Wendroff explicit scheme, providing second-order accuracy in space and time. The ions produced from the nucleus of the comet will add considerable effects on the microstructure of the solar wind, thus severely altering its physical properties. The present simulation focuses on careful analysis of these properties by means of simulating the behavior of the comet Hale-Bopp’s tail at 1 AU from the sun. These properties include the changes of the plasma density,

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Publication Date
Tue Jul 01 2025
Journal Name
Alexandria Engineering Journal
Impact of dust storms on plant biomass: Model structure and dynamic study
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Publication Date
Mon Apr 06 2020
Journal Name
Bmc Oral Health
The reliability of surgeons to avoid traumatic insertion of dental implants into high-risk regions: a panoramic radiograph study
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Abstract<sec> <title>Background

The posterior regions of the jaws usually represent a significant risk for implant surgery. A non-valid assessment of the available bone height may lead to either perforation of the maxillary sinus floor or encroachment of the inferior alveolar nerve and consequently to implant failure. This study aimed to evaluate the reliability of surgeon’s decision in appraising the appropriate implant length, in respect to vital anatomical structures, using panoramic radiographs.

Methods

Only implants that are inserted in relation to the maxillary sinus (MS) or the mandibular canal (MC) were enrolled

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Publication Date
Wed Dec 01 2021
Journal Name
International Medical Journal
Knowledge and Attitude of Iraqi Dentists towards the Use of Cone Beam Computed Tomography in Endodontics: A Questionnaire Study
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Objective: The aim of this study was to assess the knowledge and attitude of Iraqi dentists towards cone beam computed tomography (CBCT) applications in endodontics by using an online survey. Materials and Methods: A questionnaire, consisting of 31 questions, targeted general dental practitioners and specialists in different dental specialities. A total of 306 participants were included. Data were assessed according to the frequency of distribution and the chi-square test was applied to analyse the difference in responses between two independent groups. Results: Among the participants 63.4% were using digital radiography in their daily practice, and 84% had awareness about CBCT's uses, with higher statistically significant responses among e

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Publication Date
Sun Dec 01 2019
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Analysis of actuarial experience and acceptance of individual life insurance: A case study in the Iraqi General Insurance Company
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This research seeks through the adoption of two basic variables, where he considered the actuarial experience as an independent variable, while the process of accepting the risk and dimensions related to it is a dependent variable, the research was adopted to present the data achieved by the company during the life insurance business during the adoption of actuarial experience at the beginning of its work where Adoption of the historical method in the analysis of those data to prove the researcher's opinion, through the analysis of data (5 years) for the first period, which extends between (1975-1979), the period during which the company adopted the actuarial experience at the time, also taken data for the same dimensions related to the

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Publication Date
Sat Dec 15 2018
Journal Name
Journal Of The College Of Education For Women
Bayiyatan Abi Firas Al-Hamadaniy's on the horns of ad dilemma of prison and longing a stylistic analytical study
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Abstract

The current study aims to study one Firas Al- Himdani's  Romeyat poems (320 – 357 AH), he was one of sham poets in the era of the Abbasid as to know the glories of the knight and Arabic poet, whose message led to preserve the honor of the nation and Islam prestige , along with exposing the better one . His message includes Arabic merits and high values in respect of chivalry , encouragement , sacrifice , forgiveness and tolerance in addition to morality and patience .

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Publication Date
Tue Mar 03 2020
Journal Name
International Journal Of Psychosocial Rehabilitation
A Study of Some Biochemical Variables and Functional Indicators and Their Relationship to the Achievement of 200m Young Runners
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ES Hussein

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Publication Date
Wed Jun 01 2022
Journal Name
Political Sciences Journal
Terrorism and its impact on the right of Human in development - A study case of ISIS (Daesh) in Iraq
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       Iraq is one of the most important countries in the world that has received its share of terrorist acts by the terrorist organization the Islamic State of Iraq and al-Sham (ISIS), which has caused instability, especially during the period of ISIS's control of seven Iraqi provinces (2014-2017). This stage has caused a decline in the levels of human and economic development and its inconsistency with the capabilities and needs of the Iraqi population. Therefore, this study aims to investigate the hypothesis that there is a close relationship between the decline in development in Iraq and the brutal practices of ISIS that it committed during his period of control over many Iraqi cities and regions. This study used several method

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