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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 Jun 28 2024
Journal Name
Al-rafidain Journal Of Medical Sciences ( Issn 2789-3219 )
Synthesis, Characterization, Molecular Docking, ADMET Study, and Antimicrobial Evaluation of New Mannich Bases of Isatin–Thiazole Imine Bases
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Background: The isatin molecule is present in many natural substances, including plants and animals, and is used to prepare compounds with various biological activities. Objectives: To synthesize a new series of isatin derivatives with the expectation that they will have antimicrobial activity. Methods: Thiazole Schiff bases were synthesized from various Mannich bases of isatin to evaluate their antimicrobial properties. Initially, Mannich bases (2a–e) were synthesized by reacting isatin with formaldehyde and different secondary amines. Subsequently, they were treated with 2-aminothiazole to yield the final compounds (3a–e). Spectroscopic characterization was done via FT-IR and 1H-NMR. The antimicrobial screening was conducted o

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Publication Date
Mon Aug 01 2022
Journal Name
Inorganic Chemistry Communications
Study the application of new type green corrosion inhibitors for iron metal
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Density functional theory (DFT) calculations were used to evaluate the capability of Glutamine (Gln) and its derivative chemicals as inhibitors for the anti-corrosive behavior of iron. The current work is devoted to scrutinizing reactivity descriptors (both local and global) of Gln, two states of neutral and protonated. Also, the change of Gln upon the incorporation into dipeptides was investigated. Since the number of reaction centers has increased, an enhancement in dipeptides’ inhibitory effect was observed. Thus, the adsorption of small-scale peptides and glutamine amino acids on Fe surfaces (1 1 1) was performed, and characteristics such as adsorption energies and the configuration with the highest stability and lowest energy were ca

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Publication Date
Tue Sep 30 2025
Journal Name
Iraqi Journal Of Science
A Study on Using Molasses Production Waste Powder as a Green Adsorbent for Cu (II) Ions from its Aqueous Solution
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This study utilized low-cost agricultural waste (molasses production waste powder) to extract copper ions from aqueous solutions. The present investigation explored a range of factors that influence the adsorption process, including temperature, pH, ionic strength, contact time, quantity of adsorbent, and particle size. Spectrophotometric analysis was used to determine the solution's absorbance both before and after the adsorption procedure. The Langmuir and Freundlich adsorption models were used to match the equilibrium data. The Freundlich model was determined to be the best isotherm model using the linear regression coefficient R2=0.9868. Thermodynamic parameters, including enthalpy, entropy, and Gibbs free energy, were calculate

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Publication Date
Thu May 14 2026
Journal Name
Journal Of Physical Education
A Comparative Study According to Angiotensin Genetic Diversity As Indicator for 30m Freestyle Swimming in Youth aged (15 – 16) Year Old
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Publication Date
Sun Dec 31 2023
Journal Name
Revue Académique De La Recherche Juridique
Humanizing Legal Rules (The Winter Truce in France as a Model)
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Since the law is the tool for implementing the state’s public policies, it is natural that its provisions (or at least some of them) seek to preserve human dignity as the source on which all rights and freedoms are based. One of the examples of humanizing the provisions of the law in France is what is known as the winter truce. What is this truce, what are the justifications for granting it, what is its historical origin, how did the legislative treatment of it develop, what are the similarities and differences between it and other legal periods included in French law, what is the scope of its application, and what are the effects resulting from it. These questions and others are what we will try to answer through this research.

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Publication Date
Sun Dec 31 2017
Journal Name
College Of Islamic Sciences
Stylistic phenomena in the Quranic referral: (Pronouns of backbiting as a model)
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Research summary

Backbiting pronouns have gained great importance in contemporary textual linguistic studies, as they play a coordinating function in the text and link its parts.

Interpreters did not overlook the role of backbiting pronouns in achieving the function of consistency and coherence in the Qur’anic text, as they referred to this, including Ibn Ashour, who had many analytical practices related to referral issues and their complexities. The Qur'anic reference to the pronouns of backbiting, so the researcher traced these phenomena and their evidence in the Holy Qur'an, aiming to clarify their role in enriching the significance and in the coherence and harmony

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Publication Date
Sat Feb 28 2026
Journal Name
Journal Of Molecular Structure
Synthesis, Characterization, Molecular Docking and anti-corrosion activities of new Pyrimidine Derivatives
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Publication Date
Sun Mar 01 2026
Journal Name
Journal Of Molecular Structure
Synthesis, characterization, molecular docking and anti-corrosion activities of new pyrimidine derivatives
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In the present study, chalcone derivatives were synthesized via the Claisen-Schmidt condensation of 2-methyl acetanilide or 4-nitro acetanilide with p-dimethyl amino benzaldehyde in an ethanolic sodium hydroxide solution. The resulting chalcone reacted with urea or thiourea to produce several novel pyrimidine derivatives. All the synthesized compounds were characterized by FTIR, 1HNMR and 13CNMR spectroscopy. Before the synthesis process, molecular docking studies were performed to evaluate the potential of the synthesized molecules as drug candidates. Thus, molecular docking studies were performed using the CCDC GOLD suite (version 2025). The molecular docking results showed that the synthesized molecules had a noticeable affinity towards

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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
Thu May 14 2026
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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