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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 30 2023
Journal Name
Pakistan Heart Journal
Workplace Violence and Nursing Job Performance at Pediatric Emergency Departments: A Comparative Study
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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
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
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
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
Mon Jan 01 2007
Journal Name
Journal Of The Faculty Of Medicine Baghdad
Herbal activation of mammary gland; a comparative
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Seventy five adult virgin female Norway rats (60 experimental and 15 controls) were used toevaluate the effect of seeds of three herbs (Fennel, Cumin and Garden cress) on their mammaryglands. Experimental animals were fed with these herbs (each type of herb seeds was given to twentyexperimental rats) for fourteen days. Rats were sacrificed and mammary gland sections wereobtained, stained then morphometrically assessed. Serum prolactin level was performed too.Results revealed that Garden cress seeds are the strongest lactogenic agent among the three. BothFennel and Cumin seeds were shown to be very weak galactagogues.

Publication Date
Sun Jan 27 2019
Journal Name
Journal Of The College Of Education For Women
The Inauguration of Faisal Bin Al -husain as Iraq King (A Study of British Documents)
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Husain as a king of Iraq.
This paper deals with the British communication with faisel . then Winston Churchill's speech in British common house .then fodlowed by arriving faisal to Iraq after that the referend um faisel .
The his claims of British maneuver lastly coronation on faisal & his inauguration as a king of Iraq.

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Publication Date
Sat Jan 01 2022
Journal Name
Lecture Notes In Civil Engineering
Evaluation the Level of Service of Signalized Intersection: Al-Amreia Intersection as a Case Study
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Abstract<p>One of the main element in the network is the intersection which consider as the critical points because there are many conflict in this element. The capability and quality of operation of an intersection was assessed to provide a better understanding of the network's traffic efficiency. In Baghdad city, the capital of/Iraq the majority of the intersections are operated under the congestion status and with level of service F, therefore theses intersection are consider as high spot point of delay in the network of Baghdad city. In this study we selected Al-Ameria signalized intersection as a case study to represent the delay problem in the intersections in Baghdad. The intersection is located in the w</p> ... Show More
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Publication Date
Sat Oct 20 2018
Journal Name
Journal Of Economics And Administrative Sciences
Evaluation of the Quality of Health Services from Patients’ Perspective: A Comparative Study between Public and Private Hospitals
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ASTRACT

The current study aimed to identify the quality of health services provided by the Omani health sector through the comparison between public and private hospitals in Dhofar Governorate, Oman. A questionnaire has been developed to collect data from 360 patients who received health services in one public Hospital (Sultan Qaboos) and three private Hospitals (Badr Al-Sama, Lifeline, and Al-Hakeeim). The data were analyzed using independent samples T-Test and One Way ANOVA. The results of the study showed that the quality levels of health services offered in private hospitals were better than public hospitals. The study results also reveled that there are significant differences between public hospitals and private hos

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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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