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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 Mar 01 2024
Journal Name
Physical Chemistry Research
Exploring the Potential of Quantum Chemical Calculations for Synthesized Quinazoline Derivatives as Superior Corrosion Inhibitors in Acidic Environment
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Hydrochloric acid (HCl) is a substance that is frequently utilized in industrial operations for important tasks such as chemical cleaning and pickling metallic surfaces.Therefore, the corrosion inhibition ability of three newly synthesized quinazoline derivatives namely, 3-allyl-2-(propylthio) quinazolin-4(3H)-one) (APQ), (3-allyl-2-(allylthio) quinazolin-4(3H)-one) (AAQ), (3-allyl- 2-( Prop -2-yn -1-ylthio) Quinazolin - 4 (3H) - one) (AYQ) were theoretically determined and these compounds were characterized using Fourier Transform Infra-Red (FTIR) and 1H and 13C Nuclear Magnetic Resonance (NMR) spectroscopic. A series of quantum chemical properties of these derivatives: EHOMO, ELUMO, energy gap (ΔE),dipole moment (μ), hardness (η), soft

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Publication Date
Tue Jun 20 2023
Journal Name
Baghdad Science Journal
Detection of Autism Spectrum Disorder Using A 1-Dimensional Convolutional Neural Network
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Autism Spectrum Disorder, also known as ASD, is a neurodevelopmental disease that impairs speech, social interaction, and behavior. Machine learning is a field of artificial intelligence that focuses on creating algorithms that can learn patterns and make ASD classification based on input data. The results of using machine learning algorithms to categorize ASD have been inconsistent. More research is needed to improve the accuracy of the classification of ASD. To address this, deep learning such as 1D CNN has been proposed as an alternative for the classification of ASD detection. The proposed techniques are evaluated on publicly available three different ASD datasets (children, Adults, and adolescents). Results strongly suggest that 1D

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Publication Date
Sun Dec 07 2014
Journal Name
Baghdad Science Journal
The level of IL-1?, IL-10 and IL-17A in Alzheimer's disease patients: Comparative study
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The objective of this study is to evaluate the level of cytokines IL-1?, IL-10 and IL-17A in the serum of patients with Alzheimer's disease (AD), vascular dementia (VD) and down syndrome (DS). The results showed that Serum level of IL-1? was significantly increased in AD patients (3.79 ± 0.26 pg/ml) as compared with DS patients (2.78 ± 0.39 pg/ml) or controls (2.78 ± 0.22 pg/ml), while no significant difference was observed between AD and VD (3.25 ± 0.20 pg/ml) patients or between VD patients, DS patients and controls. The serum level of IL-10 was approximated in VD and DS patients and controls (3.39 ± 0.24, 2.77 ± 0.39 and 3.41 ± 0.35 pg/ml, respectively), but was significantly (P ? 0.05) increased in AD patients (5.73 ± 0.55 pg/ml

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Publication Date
Tue May 16 2023
Journal Name
Political Sciences Journal
(The role of the Security Council in Managing international crises (The Libyan crisis as a model
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The Security Council has an active role in addressing international crises and dealing with their causes. The Libyan crisis is one of the most important real tests of the Security Council and its role in maintaining international peace and security, as the Council has proven so far an ineffective role in resolving the crisis and dealing withtheir causes, which has prolonged its duration and increased its complexities and dangerous repercussions, perhaps the most prominent of which is the threat of the recently achieved cease-fire and the formation of a new transitional government led by Abdel Hamid al-Dabaiba, the growing significant obstacles facing the political process, foremost of which is the continued presence of foreign forces , m

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Publication Date
Sun Dec 16 2018
Journal Name
Al-academy
The Conceptual Representations of the Jewish Personality in the International Cinema (Munich film as a model)
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This study deals with the intellectual representations whose intellectual systems are incarnated in the Jewish personality, which is considered one of the complex intellectual systems that has caused controversy throughout the ages because of the ambiguity due to the religious and psychological factors that were reflected directly and strongly on the intellectual structure of the Jewish community in general and the Jewish - Zionist personality in particular, in an attempt (to create new dimensions embodied by intellectual representations of a human nature embodied by what that - peaceful - religiously oppressed - psychologically and socially isolated character presents, because of the curse of the peoples of the world that was a cause fo

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Publication Date
Thu Feb 08 2024
Journal Name
Engineering, Technology & Applied Science Research
The Feasibility Study Report as an Effective Tool to Evaluate Investment Projects: A Solid Waste Treatment Project as a Case Study
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Hundreds of infrastructure investment projects are inserted into the Iraqi government budget annually. Many of these projects suffer from suspension, delay in completion, corruption, or other negative issues known in Iraqi construction projects. This may harm the country's economic recovery due to allocating funds to useless projects from one or more feasibility studies' components. Therefore, the best solution is to pay attention to the feasibility study reports. This study highlights the importance of feasibility studies reports for investment projects and their effective role in evaluating project ideas to ensure an equitable distribution of a country's financial resources to the most feasible investment projects. This importance

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Publication Date
Sun Dec 04 2016
Journal Name
Baghdad Science Journal
A comparative anatomic study of leaves of the genus Stachys L. in Iraq
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The anatomic characteristics of the leaves of 22 taxa of Stachys L. representing seven of the currently recognized sections distributed in northern Iraq, were examined. The study did not found any variations in the characteristics of the stomata system of the leaves.Therewere variations with a good taxonomic value in other anatomic characteristics.Thevariations in characters of the mesophyll tissue in S.kurdica var.brevidens Bom ex Bhattacharjeewas bifacial but in S.kurdica var.kurdica Boiss. & Hohen.was unifacial .The study also found that the taxa S.benthamiana Bioss., S.lanigera (Bornm.) Rech.f. andS.kotscyi Bioss. with 3 vascular bundles in the middle vein while the taxa S.ballotiformis Vatke., S.megalodonta Hausskn. &Bo

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Publication Date
Sun Dec 04 2016
Journal Name
Baghdad Science Journal
A comparative anatomic study of leaves of the genus Stachys L. in Iraq
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The anatomic characteristics of the leaves of 22 taxa of Stachys L. representing seven of the currently recognized sections distributed in northern Iraq, were examined. The study did not found any variations in the characteristics of the stomata system of the leaves.Therewere variations with a good taxonomic value in other anatomic characteristics.Thevariations in characters of the mesophyll tissue in S.kurdica var.brevidens Bom ex Bhattacharjeewas bifacial but in S.kurdica var.kurdica Boiss. & Hohen.was unifacial .The study also found that the taxa S.benthamiana Bioss., S.lanigera (Bornm.) Rech.f. andS.kotscyi Bioss. with 3 vascular bundles in the middle vein while the taxa S.ballotiformis Vatke., S.megalodonta Hausskn. &Bornm.exP.H.Davis

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Publication Date
Sat Sep 02 2023
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Desulphurization of Simulated Oil Using SAPO-11 with CNT's as Adsorbent: A Kinetic Study
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In this study, sulfur was removed from imitation oil using oxidative desulfurization process. Silicoaluminophosphate (SAPO-11) was prepared using the hydrothermal method with a concentration of carbon nanotubes (CNT) of 0% and 7.5% at 190 °C crystallization temperature. The final molar composition of the as-prepared SAPO-11 was Al2O3: 0.93P2O5: 0.414SiO2. 4% MO/SAPO-11 was prepared using impregnation methods. The produced SAPO-11 was described using X-ray diffraction (XRD) and Brunauer-Emmet-Teller (N2 adsorption–desorption isotherms). It was found that the addition of CNT increased the crystallinity of SAPO-11. The results showed that the surface area of SAPO-11 containing 7.5% CNT was 179.54 m2/g, and the pore volume was 0.31

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Publication Date
Sat Sep 30 2023
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Desulphurization of Simulated Oil Using SAPO-11 with CNT's as Adsorbent: A Kinetic Study
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In this study, sulfur was removed from imitation oil using oxidative desulfurization process. Silicoaluminophosphate (SAPO-11) was prepared using the hydrothermal method with a concentration of carbon nanotubes (CNT) of 0% and 7.5% at 190 °C crystallization temperature. The final molar composition of the as-prepared SAPO-11 was Al2O3: 0.93P2O5: 0.414SiO2. 4% MO/SAPO-11 was prepared using impregnation methods. The produced SAPO-11 was described using X-ray diffraction (XRD) and Brunauer-Emmet-Teller (N2 adsorption–desorption isotherms). It was found that the addition of CNT increased the crystallinity of SAPO-11. The results showed that the surface area of SAPO-11 cont

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