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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
Fri Sep 01 2023
Journal Name
Journal Of Molecular Structure
Synthesis, spectral studies, DFT, biological evaluation, molecular docking and dyeing performance of 1-(4-((2-amino-5-methoxy)diazenyl)phenyl) ethanone complexes with some metallic ions
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Publication Date
Fri Sep 01 2023
Journal Name
Journal Of Molecular Structure
Synthesis, spectral studies, DFT, biological evaluation, molecular docking and dyeing performance of 1-(4-((2-amino-5-methoxy)diazenyl)phenyl) ethanone complexes with some metallic ions
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Four Co(II), (C1); Ni(II), (C2); Cu(II), (C3) and Zn(II), (C4) chelates have been synthesized with 1-(4-((2-amino- 5‑methoxy)diazenyl)phenyl)ethanone ligand (L). The produced compounds have been identified by using spectral studies, elemental analysis (C.H.N.O), conductivity and magnetic properties. The produced metal chelates were studied using molar ratio as well as sequences contrast types. Rate of concentration (1 ×10􀀀 4 - 3 ×10􀀀 4 Mol/L) sequence Beer’s law. Compound solutions have been noticed height molar absorptivity. The free of ligand and metal chelates had been applied as disperse dyes on cotton fabrics. Furthermore, the antibacterial activity of the produced compounds against various bacteria had been investigated. F

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Publication Date
Sun Mar 07 2010
Journal Name
Baghdad Science Journal
The Effect of Cyperus esculentus on Sperm Function Parameters in Prepubertal Mice as a Model for Human
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The objective of this work was to study the effect of oral administration of Cyperus esculentus (CE) and its alcoholic extract on sperm function parameters in prepubertal mice as a model for human .The animals were divided into three groups each contains 6 animals .Group 1 was treated with 150 mg/ kg body weight /day of crude CE, group 2 was treated with same dose of alcohol extract of CE and group 3 regarded as control throughout six weeks period. The results showed a significant (p> 0.05) increase in the mean of sperm concentration ,sperm motility percent and progressive sperm motility between treated groups and control . There was no differences among groups in the mean of sperm normal morphology and sperm viability . No significa

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Publication Date
Thu Apr 01 2021
Journal Name
Iop Conference Series: Earth And Environmental Science
Defining the aspects of the local urban sustainability: Eco- cities as a model
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The absence of ecological perception in the local urbanization resulted in the lack of a clear conception of achieving sustainability in its simplest form in the urban reality and in the city of Baghdad in particular. The research assumes the possibility of achieving urban sustainability in Iraqi cities by applying the cities for the most effective methods to implemented ecological solutions and introducing appropriate urban planning tools and improve the living environment. The research focuses on the ability to define some aspects to achieve a sustainable local urban identity from global experiences. This was performed by proposing a scheduled theoretical framework, through which the features of sustainability can be extrapolated from the

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Publication Date
Sun Nov 09 2025
Journal Name
Magazine Aldhakwat Albedh
The impact of atheism on the individual and society, Iraq as a model
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Atheists have spread in the modern era, so that atheism has become a bad phenomenon in the world in general and in Islamic societies in particular, so the research aims to study the individual and social effects left by atheism on the atheists themselves, and the research included multiple axes: atheism linguistically and idiomatically, atheism in the Qur’an Noble and Modern (and Contemporary) Atheism Statistics: and the reasons for atheism: Studying the phenomenon of atheism in Iraq as a model, then studying the effects of atheism: on the individual first, then atheism and its impact on society, then the conclusion, recommendations, sources and references

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Publication Date
Thu Apr 01 2021
Journal Name
Iop Conference Series: Earth And Environmental Science
Defining the aspects of the local urban sustainability: Eco-cities as a model
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Abstract<p>The absence of ecological perception in the local urbanization resulted in the lack of a clear conception of achieving sustainability in its simplest form in the urban reality and in the city of Baghdad in particular. The research assumes the possibility of achieving urban sustainability in Iraqi cities by applying the cities for the most effective methods to implemented ecological solutions and introducing appropriate urban planning tools and improve the living environment. The research focuses on the ability to define some aspects to achieve a sustainable local urban identity from global experiences. This was performed by proposing a scheduled theoretical framework, through which th</p> ... Show More
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Publication Date
Tue Jun 01 2021
Journal Name
Political Sciences Journal
The European Union and the Extremist Right Phenomenon: Brexit as a Model
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The European Unit has never been affected by a serious phenomena as the phenomena of the advancing of the far right parties. Though these parties vary in their impact in their original countries, they agree on one important issue which is the deconstruction of the European unit and limiting its supernational powers. These increasing popular parties aim at more national independence in decision making away from the decisions taken by Brussels. Moreover, they criticize the financial and administrative corruption accompanied many of the rescuing procedures directed for example towards countries like Greece and Spain during the international economic crisis. This failure nourishes many of the negative feelings against the European unit which

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Publication Date
Tue Dec 01 2015
Journal Name
Journal Of Economics And Administrative Sciences
Developing Human Capital according to the Communities of Practice: A comparative study by using Data Envelopment Analysis
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The research discusses the need to find the innovative structures and methodologies for developing Human Capital (HC) in Iraqi Universities. One of the most important of these structures is Communities of Practice (CoPs) which contributes to develop HC by using learning, teaching and training through the conversion speed of knowledge and creativity into practice. This research has been used the comparative approach through employing the methodology of Data Envelopment Analysis (DEA) by using (Excel 2010 - Solver) as a field evidence to prove the role of CoPs in developing HC. In light of the given information, a researcher adopted on an archived preliminary data about (23) colleges at Mosul University as a deliberate sample for t

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Publication Date
Sun Jul 17 2022
Journal Name
Al–bahith Al–a'alami
Post-interactive communication A study to build a model for the flow of communication in social networking sites
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The issue of the research lies in the non-representation of the models developed for the communication process in the interaction and networking processes through social media, as the research sought to build a network model of communication according to the specific data and features of social media platforms in order to reach a special generalization to understand how the process of networking operates in cyberspace.

The researcher followed the analytical survey approach as she described the communication models outwardly in order to be able to build a networked communication model that represents the flow of post-reactive communication. Therefore, it has been named "Nebula - Sadeem" after the concept of post-space and cosmic g

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Publication Date
Tue Apr 30 2019
Journal Name
International Journal Of Environmental Research
A Comparative Study for the Identification of Superior Biomass Facilitating Biosorption of Copper and Lead Ions: A Single Alga or a Mixture of Algae
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