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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
Sun Mar 01 2020
Journal Name
Iop Conference Series: Materials Science And Engineering
Spectral fluctuations in <sup>24</sup>Mg nucleus using the framework of the nuclear shell model
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Abstract<p>Random matrix theory is used to study the chaotic properties in nuclear energy spectrum of the <sup>24</sup>Mg nucleus. The excitation energies (which are the main object of this study) are obtained via performing shell model calculations using the OXBASH computer code together with an effective interaction of Wildenthal (W) in the isospin formalism. The <sup>24</sup>Mg nucleus is assumed to have an inert <sup>16</sup>O core with 8 nucleons (4protons and 4neutrons) move in the 1d<sub>5/2</sub>, 2s<sub>1/2</sub> and 1d<sub>3/2</sub> orbitals. The spectral fluctuations are studied by two statistical measures: the nearest neighb</p> ... Show More
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Publication Date
Tue Jun 30 2020
Journal Name
Journal Of Economics And Administrative Sciences
The Relationship between Fiscal Policy and Human Development Analytical Studay Of Iraq Using The (ARDL)Model
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Fiscal policy is one of the important economic tools that affect economic development in general and human development in particular through its tools (public revenues, public expenditures, and the general budget).

It was hoped that the effects of fiscal policy during the study period (2004-2007) will positively reflect on human development indicators (health, education, income) by raising these indicators on the ground. After 2003, public revenues in Iraq increased due to increased revenues. However, despite this increase in public budgets, the actual impact on human development and its indicators was not equivalent to this increase in financial revenues. QR The value of the general budget allocations ha

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Publication Date
Thu Dec 25 2025
Journal Name
Retos
The effect of neurofeedback on free throw accuracy in female basketball players of Baghdad University
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Background: Female basketball players often face difficulties in maintaining free throw accuracy, particularly under psychological and neural pressure. Traditional training emphasizes physical skills, often neglecting cognitive and neurophysiological factors essential for precision performance. Objective: This study examined the effect of neurofeedback training on free throw accuracy in female basketball players at the University of Baghdad, comparing outcomes between an experimental group and a control group, and assessing associated neural changes. Methods: A quasi-experimental design involved two groups: an experimental group receiving neurofeedback to regulate brainwave activity, and a control group undergoing traditional traini

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Publication Date
Sun Mar 27 2022
Journal Name
Sport Tk-revista Euroamericana De Ciencias Del Deporte
Effect of resistance training on the biomechanics and accuracy of serve receiving skills in volleyball
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This study aimed to identify the effect of resistance training on the biomechanics and accuracy of serve receiving skills in volleyball. The research community was composed of 26 young volleyball players of Baghdad volleyball clubs. A total of 4 players were selected for the preliminary experiment, while 14 participants were recruited as the main sample for the study. In the present study, a set of resistance exercises were designed by the researchers for the volleyball players of the sample. Exercises were performed by the sample participants during the course of study. The biomechanical variables considered in the present study were: Preparation moment (shoulder joint angle, hip angle, knee joint angle), moment of pr

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Publication Date
Mon Jun 01 2020
Journal Name
International Journal Of Agricultural And Statistical Sciences
The effect of some herbicides on the companion weed to three cultivars of oats
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A field experiment was carried out to find out the effect of some herbicides(Pallas, Crash, U46) on the companion weed to three cultivars of the oat crop (Shefa, Hamel, and Pimula) and the yield and its components of these cultivars. The results showed the superiority of the two treatments of spraying weed herbicides (T1 and T2 ) by giving the best results, as they recorded the lowest number of weed plants after 30 days of spraying reached 1.44 and 1.67 plant/m2 . Besides, the lowest weed dry weight was 0.11 and 0.00 g/m2, and the highest inhibition percentage in dry weight was 98.44% and 100.0% of the two treatments, respectively. The treatment T2 was also superior by giving the highest control percentage of 93.28% compared to the compari

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Publication Date
Thu Jul 25 2024
Journal Name
Metals
The Effects of Three Antibacterial Nanoparticle Coatings on the Surface Characteristics of Stainless Steel
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The aim of this study is to investigate the antibacterial capabilities of different coating durations of three nanoparticle (NP) coatings: molybdenum (Mo), tantalum (Ta), and zinc oxide (ZnO), and their effects on the surface characteristics of 316L stainless steel (SS). The coated substrates underwent characterization utilizing field emission scanning electron microscopy (FE-SEM), energy dispersive X-ray spectrometry (EDX), and X-ray diffractometer (XRD) techniques. The antibacterial efficacy of NPs was evaluated using the agar diffusion method. The FE-SEM and EDX images confirmed the presence of nano-sized particles of Mo, Ta, and ZnO on the surface of the substrates with perfectly symmetrical spheres and a uniform distribution of

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Publication Date
Wed Feb 18 2026
Journal Name
Al–bahith Al–a'alami
The Role of Media Coverage of the Iraqi Satellite Channels in Shaping Public Attitudes towards Terrorism (a Field Study of a Sample of an Audience of the City of Baghdad)
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Violence is one of the most serious threats facing societies because it affects their internal structure and threatens the security and stability of society. It is classified as one of the types of security crises that are emerging in Arab and Islamic societies in particular, and in most countries of the world in general.

The threat of this crisis is increasing. Terrorism is considered as one of the most serious aspects of that all the countries of the world, currently, suffer from. The terrorism has begun to penetrate deep into society in one way or another starting from the Second World War, which led to the emergence of leftist movements in Western Europe, Japan, France, Italy and other countries as a result of emerging ideas

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Publication Date
Wed Aug 19 2020
Journal Name
Applied Water Science
Spiral path three phase fluidized bed reactor for treating wastewater contaminated with engine oil
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Abstract<p>In this study, a new type of circulating three-phase fluidized bed reactor was conducted by adding a spiral path and was named as spiral three-phase fluidized bed reactor (TPFB-S) to investigate the possibility for removing engine oil (virgin and waste form) from synthetic wastewater by using Ricinus communis (RC) leaves natural and activated by KOH. The biosorption process was conducted by changing particle diameter in the range 150–300 and 300–600 µm, liquid flow rate in the range 2.5–4.5 L/min and gas flow rate in range of 0–1 L/min, while other parameters initial oil emulsion concentration, pH, adsorbent concentration, agitation speed and contact time were kept constant at 2000 mg/L, 2,</p> ... Show More
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Publication Date
Wed Dec 27 2023
Journal Name
Journal Of Planner And Development
The dynamics of the oil industry in shaping land uses: a case study of the Zubair oil field
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The emergence of oil fields and subsequent changes in adjacent land use are known to affect settlements and communities. Everywhere the industry emerges, there is little understanding about the impact of oil fields on land use in the surrounding areas. The oil industry in Iraq is one of the most important industries and is almost the main industry in the Iraqi economic sector, and it is very clear that this industry is spread over large areas, and at the same time adjoins with population communities linked to it developmentally.

The rapid development and expansion of oil extraction activities in various regions has led to many challenges related to land-use planning and management. Here, the problem of research  arises on th

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Publication Date
Sun Feb 17 2019
Journal Name
Iraqi Journal Of Physics
Nucleon momentum distributions and elastic electron scattering form factors for 58Ni, 60Ni, 62Ni, and 64Ni isotopes using the framework of coherent fluctuation model
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The nucleon momentum distributions (NMD) and elastic electron scattering form factors of the ground state for some 1f-2p-shell nuclei, such as 58Ni, 60Ni, 62Ni, and 64Ni
isotopes have been calculated in the framework of the coherent fluctuation model (CFM) and expressed in terms of the weight function lf(x)l. The weight function (fluctuation function) has been related to the nucleon density distribution (NDD) of the nuclei and determined from the theory and experiment. The NDD is derived from a simple method based on the use of the single particle wave functions of the harmonic oscillator potential and the occupation numbers of the states. The feature of the l

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