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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 18 2021
Journal Name
Review Of International Geographical Education Online
Chomsky's Political Views as a Case Study in a Critical Discourse Analysis of Ideology in the Iraqi Wars
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APDBN Rashid, Review of International Geographical Education Online (RIGEO), 2021

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Publication Date
Fri Mar 26 2021
Journal Name
Chemical Papers
DFT, anticancer, antioxidant and molecular docking investigations of some ternary Ni(II) complexes with 2‑[(E)‑[4‑(dimethylamino) phenyl]methyleneamino]phenol
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The biological activities of some ternary nickel complexes with a Schiff base obtained from 4-dimethylaminobenzaldehyde and 2-aminophenol have been reported. The Schiff base ( HL1) acts as a primary ligand whereas, anthranilic acid ( HL2), 2-nitroaniline ( HL3), alanine ( HL4) and histidine ( HL5) act as secondary ligand or co-ligand. The anticancer activity of these compounds was studied against human colon carcinoma (HCT-116), human hepatocellular liver carcinoma (HEPG-2) and human breast carcinoma (MCF-7) cell lines. As per the results, the compounds were active against the cell lines. The antioxidant activity of the same compounds was evaluated using DPPH (1,1-diphenyl-2-picryl-hydrazyl) radical scavenging and compared with ascorbic aci

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Publication Date
Mon Jun 19 2023
Journal Name
Journal Of Engineering
Removal of Water Turbidity by using Aluminum Filings as a Filter Media
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The ability of using aluminum filings which is locally solid waste was tested as a mono media in gravity rapid filter. The present study was conducted to evaluate the effect of variation of influent water turbidity (10, 20and 30 NTU); flow rate(30, 40, and 60 l/hr) and bed height (30and60)cm on the performance of aluminum filings filter media for 5 hours run time and compare it with the conventional sand filter. The results indicated that aluminum filings filter showed better performance than sand filter in the removal of turbidity and in the reduction of head loss. Results showed that the statistical model developed by the multiple linear regression was proved to be
valid, and it could be used to predict head loss in aluminum filings

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Publication Date
Fri Jun 21 2024
Journal Name
Pharmacia
Synthesis and biological activity evaluation of new isatin-gallate hybrids as antioxidant and anticancer agents (in vitro) and in silico study as anticancer agents and coronavirus inhibitors
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Background: The hybrid compounds hold promise for developing novel pharmaceuticals, potentially exhibiting greater activity, mainly against viruses and cancer diseases, than their components.

Objective: In this study, researchers explored the potential synergistic effects of hybrid molecules by designing and synthesizing a series of isatin-gallate hybrids, denoted as N’-(5-substituted-2-oxoindolin-3-ylidene)-3,4,5-trihydroxybenzohydrazide (3a–d).

Methods: Isatin-gallate hybrids (3a–d) were synthesized by reacting gallic hydrazide with each of the isatin analogs (2a–d). The structures of all produced comp

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Publication Date
Sun Mar 01 2015
Journal Name
Baghdad Science Journal
The Effect of Age and Gender on Fetuin-A and Some Biochemical parameters in Blood Sera of Iraqi patients with T2DM: A comparative study
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The serum protein test includes measurement of the level of total protein(albumin, globulin). Fetuin-A is a blood protein made in liver. It can inhibit insulin receptor, enhance insulin sensitivity and make the individuals more likely to develop type 2 diabetes, then disorder in lipid profile (Total cholesterol(TC), low density lipoprotein cholesterol (LDL-c), high density lipoprotein cholesterol (HDL-c), Triglyceride(TG) and very low density lipoprotein cholesterol (VLDL-c) . To evaluate Fetuin-A, total protein, albumin, globulin, HbAlc and lipid profile in 200 adult and elderly Iraqi patients with type 2 Diabetes Mellitus were taken and compare them with 200 subjects as a healthy control. The laboratory analysis(for patients and

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Publication Date
Wed Nov 20 2024
Journal Name
Naunyn-schmiedeberg's Archives Of Pharmacology
The potential role of targeting the leptin receptor as a treatment for breast cancer in the context of hyperleptinemia: a literature review
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Since cancer is becoming a leading cause of death worldwide, efforts should be concentrated on understanding its underlying biological alterations that would be utilized in disease management, especially prevention strategies. Within this context, multiple bodies of evidence have highlighted leptin’s practical and promising role, a peptide hormone extracted from adipose and fatty tissues with other adipokines, in promoting the proliferation, migration, and metastatic invasion of breast carcinoma cells. Excessive blood leptin levels and hyperleptinemia increase body fat content and stimulate appetite. Also, high leptin level is believed to be associated with several conditions, including overeating, emotional stress, inflammation, obesity,

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Publication Date
Wed Jul 17 2019
Journal Name
Aip Conference Proceedings
The correction of the line profiles for x-ray diffraction peaks by using three analysis methods
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In this study used three methods such as Williamson-hall, size-strain Plot, and Halder-Wagner to analysis x-ray diffraction lines to determine the crystallite size and the lattice strain of the nickel oxide nanoparticles and then compare the results of these methods with two other methods. The results were calculated for each of these methods to the crystallite size are (0.42554) nm, (1.04462) nm, and (3.60880) nm, and lattice strain are (0.56603), (1.11978), and (0.64606) respectively were compared with the result of Scherrer method (0.29598) nm,(0.34245),and the Modified Scherrer (0.97497). The difference in calculated results Observed for each of these methods in this study.

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Publication Date
Sun Dec 27 2020
Journal Name
Journal Of The College Of Education For Women
Using the Image in Teaching Arabic Language Vocabulary to Non-Native Speakers: The Experience of the Arabic Language Institute - King Abdul-Aziz University - as a Model: آمال موسى عباس الإمام
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The study aims to demonstrate the importance of instructional methods in teaching Arabic language as a second language or teaching the Arabic language to non-native speakers. The study is in line with the tremendous development in the field of knowledge, especially in the field of technology and communication, and the emergence of many electronic media in education in general and language teaching in particular. It employs an image in teaching vocabulary and presenting the experience of the Arabic Language Institute for Non-Speakers-King Abdul-Aziz University. The study follows the descriptive approach to solve the problem represented by the lack of interest in the educational methods when teaching Arabic as a second language. Accordingl

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Publication Date
Thu Apr 01 2021
Journal Name
Iop Conference Series: Earth And Environmental Science
Reality analysis of the state of spatial distribution of green areas using geographic information systems (GIS) – The holy city of Najaf as a case study
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Abstract<p>Green areas are an essential component of city planning, as they serve as an outlet for them to spend their free time, in addition to the environmental role that these green areas play in improving the city’s climate by purifying the air and beautifying the city. The study’s problem is summarized in identifying the appropriateness of the current spatial distribution of green areas in the city of Najaf with the current population densities and the pattern in which green areas are distributed using GIS and knowing the per capita share of those green areas in the city, the research assumes that the inconsistency of spaces between regions Green and residential neighbourhoods need to c</p> ... Show More
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Publication Date
Wed Dec 11 2019
Journal Name
Journal Of The College Of Education For Women
A Comparative Study in the (myth of Pygmalion) between Bernard Shaw and Sadik Hidayat: University of Ferdowsi - Iran
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  In our time, not too long ago, the universities of the world have been fast to take care of the study of an innovative type of technical and human studies, called the science of "comparative literature". Comparative research studies have grown and flourished rapidly in response to the demands of both mental and artistic life. This shows the increasing awareness at both the modern national and the international levels in order to develop through connecting with the international intellectual, nental and artistic currents to nurture ethics and originality. Comparative studies show that the beginning of the comparative literature goes back to the time when the Latin literature was connected to the Greek literature and th

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